Burns Verkaufen der Kraftwerk - S3-E11
Continuity mistake: There are several errors in the plant's parking lot: 1, in the overhead shot of the plant, we see Homer drive in, and there are parking barriers on the road. These disappear in the next shot. 2, As he drives in, there are at least eleven parking spaces on the right side of him. Carl takes up one spot, and in the next shot there are about 3 parking spaces left. 3, When he parks, we see several cars behind him, but in the shot before that, no cars are visible, not even parking spaces, and 4, when both Homer and Carl drive in, we see orange lines on the road, which weren't visible in any other part of the scene. (00:07:00)

Continuity mistake: When Barney enters the tavern, we see a guy working with Moe. His hands change position between shots. (00:16:15)
Tree House of Horror II: A Simpsons Halloween - S3-E7
Continuity mistake: When Homer gets turned into a jack-in-the-box, we don't hear the chair he was just holding crash onto the floor. Bart doesn't make it vanish, as we see it on the floor when Homer is turned into a jack-in-the-box. (00:13:20)

Continuity mistake: There are many mistakes when Homer is checking for donut flavors, i.e. the positions of the donuts, the topping, etc. (00:03:50)

Continuity mistake: After Bart finds out that Lisa took the teacher's books, his Hall Monitor sash disappears and reappears for several shots. (00:20:05)

Like Father, Like Klown - S3-E6
Continuity mistake: At the end of Krusty's story, Homer changes from being in his tuxedo to being in his normal clothing. (00:10:10)
Suggested correction: It should be noted that a considerable amount of time has passed while Krusty is telling his story. Note the candles in the screenshot for example, they have burnt out during the story. Its reasonable to assume that there would have been a chance for them to change during this time.

Continuity mistake: When Edna sits at her desk saying "Oh, Woodrow. How could you stand me up?" the clock reads 3 O'clock. Seconds later, as Bart talks with Edna, the clock reads 4 O'clock. (00:16:45)

Continuity mistake: Nelson makes a hole in the Honor Roller during the finals. This hole disappears and reappears between shots. (00:20:00)

Continuity mistake: When Dave gives Homer the Bill Cosby book, the cover is light blue. When he reads the book in the garage, it is green. (00:09:40 - 00:11:30)
Continuity mistake: When Otto is playing the guitar with bart in the middle of the night, there are close-ups of Otto whenever he is singing. You can see that the wall behind him is plain. However, when there is a wide shot of otto and bart, the wall behind otto has two tables leaned against them. (00:15:50)

Continuity mistake: When Bart uncovers the photo of the Simpsons behind the books in Lisa's locker, the books change between shots.
Continuity mistake: When Bart and Skinner are checking lockers, you can see in a wide shot that Bart needs to check seven lockers before he gets to Lisa's locker. However, Bart checks eight lockers and then opens Lisa's locker. (00:19:35)
Continuity mistake: In the cafeteria scene where Milhouse shoots a spitball at Kearney, in the shot when Milhouse says, "We have order, but at what price," Milhouse, Lewis and the bullies all change positions at their tables. You may have to watch this part several times to understand it. (00:16:45)
Continuity mistake: When the salt spills on Milhouse's food, the table full of kids in the background has disappeared. (00:10:45)
Continuity mistake: In the garage, Martin walks behind Lewis and the other kid. He jumps to walking in front of them in the next shot. (00:09:05)
Continuity mistake: After Bart cleans his hands with a cloth after going to the private toilet, he puts it on his shoulder. A couple of shots later it has disappeared.
Continuity mistake: At the end of the episode, Bart is writing lines, and he has already written on one half of the board. On the half he has already written lines on, the lines go down the board about 3/4 of the way, yet when the shot changes, the lines now go all the way down to the bottom of the board. (00:20:35)
Continuity mistake: In the scene at the beginning when the Simpsons are eating dinner, Marge and Homer's plates are empty, then they have food on them, then they are empty again. (00:03:40 - 00:04:30)

Continuity mistake: When Mr. Burns tells Smithers that Homer is the next employee of the month, his huge red chair he was just sitting in has disappeared, and Mr. Burns is in a different position. (00:10:30)

Continuity mistake: When Homer apologizes to Moe at the end, he comes in while the door is left open. It remains closed for the rest of the scene. (00:21:05)