Plot hole: Throughout the series, auxiliary characters are always far too willing to give all kinds of information to Tru. Doctors and registrars constantly give her privileged information about patients and students. Tru is often able to retrieve information like addresses and phone numbers from people's service and utility companies, when normally you must verify your own information before they will even talk to you about your account. Of course there can't be an episode if Tru doesn't quickly find the person who asked for her help, even though she doesn't usually know much more than their name, but it's still a bit conspicuous.
Shrink Rap - S5-E2
Plot hole: The man plays his last nickel and wins the jackpot. You have to play the maximum number of coins to hit the huge jackpot which on that machine states is 5 coins.
What Is And What Should Never Be - S1-E20
Plot hole: How in the world could Keith be hired as a teacher? Not only is he a college drop-out with no teacher training, Dan mentions just an episode or two earlier how Keith is incapable of using modern machinery (specifically saying how every high school graduate will be more qualified than Keith).
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?
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).
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.
Orpheus in the Undergrowth - S2-E2
Plot hole: When Jeremy stopped to drink his water, which turned out to be vodka and which killed him via a heart attack, why did he hide himself away, surrounded by plants and only found by his mobile ringing? And why would he put the lid back on the bottle in the throes of a heart attack?
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.
Plot hole: Towards the end of the episode, Mr. Alderman ties up Cherry Peck and forces Matt to cut off Cherry's male genetalia. Matt does so, and Cherry screams in pain. Later on that night (probably at least an hour later in what would be "real time"), Mr. Alderman and Matt drive to a secluded area and Mr. Alderman forces Matt to bury Cherry alive. Matt refuses, and Cherry eventually steps out of the grave and strikes Mr. Alderman with a shovel before shooting him. Cherry has the same clothes on, but is in no sign of pain, or is even bloodied from the earlier trauma. It is safe to assume that neither Matt nor especially Mr. Alderman would have driven Cherry to any hospital, nor would any hospital even have let her out in an hour or two's time after an injury like that.
Plot hole: Gaeta and Tigh both reference the fact that the Galactica crew computes the changes in stellar drift for FTL jumps and then sends out the info to the rest of the fleet for their use. However, when they fail to rendezvous with the fleet after the emergency jump, Gaeta realizes a mistake has been made and says that Galactica's info is out of date. This creates a major plot hole because if Galactica sends out the new info to the fleet, Galactica would always have the most up to date info for FTL jumps. The crew would be able to solve the lost fleet crisis by simply reloading the last coordinates that Galactica sent out and jumping there where the fleet would be waiting for them. There would be no need to go back to the previous coordinates and recompute the jump.
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.
Plot hole: Tori somehow knows who Marah and Kapri are, despite never meeting them before.