Episode 1
While the Munsters are always said to live in the city of Mockingbird Heights, the close-up of this envelope from the Dalys shows a city that sort of looks like "Glenwood." The postmark is also for late-October, but the Munsters somehow didn't celebrate Thanksgiving until episode 6.
Episode 1
As Herman's King Arthur helmet is removed, part of the hairpiece he is wearing gets caught on it to reveal that Herman is actually bald and wearing a wig, Dr. Frankenstein did not sew his hair on very well, or that no one caught this error before the episode was edited. 
Episode 2
For this episode, Grandpa's nose is unusually long. This nose extension appears in all the pilots as well, but this is the only aired version.
Episode 2
As Eddie runs home from school being chased by a flock of girls, his widow's peak is missing. The only other time Eddie appears this way is in the three unaired pilots.
Episode 2
When looking outside to see where Grandpa threw the last of his love potion in Mrs. Cribbens' cabbages, Lily and Herman look out the window on the wrong side of the house. To see Mrs. Cribbens' house, they would have needed to go to the other side of the kitchen.
Episodes 3 and 70
Both of these episodes feature a kitchen sequence where Grandpa's electricity experiments cause the mixer, blender and rotisserie to spin out of control and the chicken/dodo on the rotisserie to fly out the window.
Episodes 4 and 6
Meeting Herman in situations without his glasses, the Munsters' family doctor, Dr. Dudley, thinks Herman has a dog (because of Herman's furry hands). Later in the episodes, Herman's hands randomly switch between being furry and normal. After these episodes, his hands are not shown as furry ever again.
Episodes 4 and 11
In these two episodes, we get a rare view of the Munsters original family car, a black limousine. After episode 11, it is never seen again. The car was actually owned by Bob Mosher.
Episode 5
In this single shot of Herman in the lab, the film has been flipped backwards (as Herman's scar is on the wrong side) probably because the original shot had Herman looking the wrong way.
Episode 5
Thing makes a brief cameo in Grandpa's cauldron before realizing that its on the wrong show.
Episode 6
Filming on the Universal lot for this exterior shot, looking into the house we can see that there really isn't anything in there besides a staircase with no creature statue on the newel post.
Episodes 7, 20 and 70 Mockingbird Heights Elementary sure does go through principals quickly, with each of these episodes showing a new one. While two principals in two years seems believable, it does seem odd the school would would have two different ones within the same school year.
Episode 9
What happened to Mrs. Cribbens? Living next door to the Munsters is now eccentric widow, Mrs. Cartwright, who Lily talks about as though she's lived there for quite some time.
Episode 10
Perhaps the most infamous Munster blooper is in this episode, when during the opening scene, a man in a white T-shirt walks in the background where the kitchen should be, next to what appears to be a metal folding chair.
Episode 11
During the outdoor scenes with Lily, Grandpa, Marilyn and Eddie in the Koach searching for Herman, all of the dialogue was post-dubbed. Listening closely to Marilyn, it's actually Pat Priest's voice coming out of Beverley Owen, who had already left the show by the time of the voice recordings. (PLAY)
Episode 13
Beverley Owen makes her last appearance as Marilyn before leaving Hollywood for New York to marry her boyfriend.
Episode 14
Stepping in as the new Marilyn, Pat Priest makes her first appearance. Perhaps to ease the transition, she only appears in the final scene and doesn't receive lines until the next episode.

Episode 16 and Munster, Go Home!
A rather large bit of plot that occurs on the ship segment of Munster, Go Home! seems strikingly familiar to what happened a few years ago in episode 16 when the Munsters went camping. As in episode 16, Lily goes to talk to Grandpa as a wolf in his cage and is unable to take him back with her. Also as in the episode, Herman busts Grandpa out of the cage freaking people out and Lily wears Grandpa as a shawl to get by uniformed officials. While the nutty event happening twice could be pretty likely for a family like the Munsters, one wonders why none of them comments on the fact that it had happened before.
Episode 20
In Igor's big episode, he is a very large bat compared to his appearances in previous episodes. Perhaps Grandpa perfected the growth potion he gave Eddie in episode 19.
Episode 23
Herman's detective sketch in this episode was actually done by Fred Gwynne.
Episode 25
On the close-up shot of Googie giving Herman a handshake with the joy buzzer, Googie's hand does not appear to be that of a young boy.
Episodes 26 and 50
While it is actually Yvonne De Carlo singing in episode 26, she is only strumming the motions on the harp. Fred Gwynne in episode 50, though, is both singing and playing the guitar during his "Dry Bones" song.
Episode 28
The shot of the ceiling for this scene reveals it to actually be made of some sort of fabric. If only Herman had noticed sooner, he would have realized that a fake ceiling is a sure sign of villainy.
Episode 29
Ken Hunt, Butch Patrick's step-father, makes an appearance in this episode as the baseball catcher who says he's going back to the minors. In real life, he did actually play in the minor and major leagues.

Episode 30 and Munster, Go Home!
The entryway and patio of the Moresbys that Marilyn visits while in England sure do look strangely similar to the Mockingbird Heights Country Club's inside and patio from episode 30. It must be a favored design for the buildings of snobs.
Episode 32
Apparently the Egyptians were even more inventive than we thought. On the sarcophagi Herman opens in the museum, they both have hinges on them--even the one that hasn't even been opened in thousands of years.
Episode 36
As Herman and Grandpa work furiously in the garage to build the Drag-u-la, Lily and Marilyn are at the sink doing dishes. Looking out the window above the sink, they act as though they can see the garage, but in reality they would need to be facing the opposite wall of the kitchen.
Season 2 Opening Credits
After Herman busts through the doors, the outline he makes doesn't match the outline we see when everyone else exits (note the extra missing piece of wood). The broken pieces of the doors on the ground are also absent when everyone exits. To actually film this sequence, the doors that Herman breaks were made of balsa wood.
Episode 42
The police officer here meeting the pigeons is actually Yvonne De Carlo's then-husband, stunt man Robert Morgan.
Episode 43
The shots showing the black shot-put and discus flying over the treetops are actually recycled footage of the baseball and football flying over the treetops from episode 29. Either that, or Grandpa transformed the objects mid-air and then changed them back so that they could hit that woman's car. 

Episode 44
The $1,000 checks that Herman and Lily write that we see at the bank aren't the same ones later stamped with "Insufficient Funds." Lily's goes from being check no. 136 to no. 108 and doesn't even have the same signature (Lily Dracula Munster vs. Mrs. Herman Munster). One suspects that perhaps the account indeed had enough money, but, as is typical in Mockingbird Heights, a crooked bank worker forged the checks and stole it all.
Episode 53
Clyde's contraption punches Herman in the right side of his face, but when he comes home later, his left eye is blackened to cleverly match Eddie's own black left eye.
Episode 55
Dr. Dudley, one of the show's few reoccurring characters besides the five Munsters, makes his fourth and final appearance. The difference is that this time he is played by Dom DeLuise, as for unknown reasons, Paul Lynde was unavailable.
Episode 57
As Grandpa experiments with his machine to send electricity to Lily's beauty parlor, he blows up the exact same lights in the park he blew up with his machinery in episode 3. Conveniently, the exact same people are standing in the exact same spots nearby to witness. 
Episode 60
Amongst all of Eddie's prizes from the "I Like Zombo Because..." Contest are two cardboard cutouts of Zombo. Besides wondering why are there two of them, the bigger question is why does one of them say, "To Eddy"?
Episodes 66 and 69
Herman's driver's license not only completely changes in the span of three episodes, but it also changes to say, "Mockingbird Hights" instead of "Heights."
Episode 67
When Herman is first painting the line down the center of the house, he is in the "inner" part (with access to the left side of the stairs and the living room sofa) and Grandpa is in the "outer" part (with access to the right side of the stairs and the telephone). The next time we see the two of them, they are on opposite sides and remain so until Lily makes them stop their petty fighting.
Episode 69
Lying in the water after getting hit, Herman's hair piece comes loose.
Munster, Go Home!
Adding to Aunt Effigie's sinister personality is the fact that she doesn't seem to actually require corrective eye wear. In different scenes, she is seen wearing her monocle on both her left and right eyes. It's a wonder that the Munsters didn't catch on to her sooner.
Episode List
1. Munster Masquerade  2. My Fair Munster  3. A Walk on the Mild Side  4. Rock-a-Bye Munster  5. Pike's Pique  6. Low Cal Munster  7. Tin Can Munster  8. Herman the Great  9. Knock Wood, Here Comes Charlie  10. Autumn Croakus  11. The Midnight Ride of Herman Munster  12. The Sleeping Cutie  13. Family Portrait  14. Grandpa Leaves Home  15. Herman's Rival  16. Grandpa's Call of the Wild  17. All-Star Munster  18. If a Martian Answers, Hang Up  19. Eddie's Nickname 20. Bats of a Feather  21. Don't Bank on Herman  22. Dance with Me, Herman  23. Follow That Munster  24. Love Locked Out  25. Come Back, Little Googie  26. Far Out Munsters  27. Munsters on the Move  28. Movie Star Munster  29. Herman the Rookie  30. Country Club Munster  31. Love Comes to Mockingbird Heights  32. Mummy Munster  33. Lily Munster, Girl Model  34. Munster the Magnificent  35. Herman's Happy Valley  36. Hot Rod Herman  37. Herman's Raise  38. Yes, Galen, There is a Herman  39. Herman's Child Psychology  40. Herman the Master Spy  41. Bronco Bustin' Munster  42. Herman Munster, Shutter Bug 43. Herman, Coach of the Year  44. Happy 100th Anniversary  45. Operation Herman  46. Lily's Star Boarder  47. John Doe Munster  48. A Man for Marilyn  49. Herman's Driving Test  50. Will Success Spoil Herman Munster?  51. Underground Munster  52. The Treasure of Mockingbird Heights  53. Herman's Peace Offensive  54. Herman Picks a Winner  55. Just Another Pretty Face  56. Big Heap Herman  57. The Most Beautiful Ghoul in the World  58. Grandpa's Lost Wife  59. The Fregosi Emerald  60. Zombo  61. Cyrano de Munster  62. The Musician  63. Prehistoric Munster  64. A Visit from Johann  65. Eddie's Brother 66. Herman the Tire Kicker  67. A House Divided  68. Herman's Sorority Caper  69. Herman's Lawsuit 70. A Visit from the Teacher
 

SOURCES

Cox, Stephen. The Munsters Television's First Family of Fright. Contemporary Books, Chicago: 1989.