Plot hole: It's revealed at the end of the episode that the reason Tommie was sleep walking was because he was so nervous about the 5th grade test. However, he was sleep walking before news about it was given (ie: The beginning of the episode).
Plot hole: People who do not have their souls retrieved, before they are killed, will suffer the effects of the death on their soul, eg. the autopsied man has scars and cuts on his soul. So how come the woman who was crushed by a piano (whose soul was only ever retrieved afterwards) is unharmed in soul form?
The New Era - S2-E4
Plot hole: Early in the episode, Alex tells Seth that the night of the Killers concert is her night off. (She works at The Bait Shop, the concert venue.) At the end of the episode, Alex is paying The Killers, as if she were the manager on duty.
Plot hole: In "Little Britain Abroad", Marjorie swaps places with another Fat Fighter from somewhere called "Rocksprings" in America. In the first episode, when Marjorie is pushed into a police car by the sheriff, it says "Miami Dade". However, in the second episode, the American Fat Fighter, Blanche, says that she is from Rocksprings, Texas, not Miami.
Worlds Collide: Part 3 - S3-E6
Plot hole: In their previous encounters with the Triceratons, the Turtles had to learn the hard way that the Triceratons breathe not oxygen but a combination of nitrogen and sulfur, which is detrimental to most Earth lifeforms, and thus had to wear special rebreathers. When the Turtles, Splinter, April and Casey enter Zanramon's throne room along with Traximus, none of them wear any breathing equipment to protect themselves from the hostile atmosphere.