Plot holes: Z often established that people can't keep their bodies if they go to hell, which GT contradicts (particularly noticable in the Super 17 arc.).
Continuity: Dr. Myuu is supposedly a Tuffle/Tsfuru, but had blue skin and an all-around awkward, non-human appearance. But all other Tuffles/Tsfuru-jins look EXACTLY the same as humans.
Plot holes: Krillin has aged into an old man yet Yamcha and Tien, who are OLDER than Krillin, have not.
Plot holes: Goku goes Super Saiyan while he has a tail in this series. According to Z, this was impossible.
Plot holes: Goku finds Super Android 17 by tracking his Ki. Androids don't have a Ki.
Plot holes: In the final episode, Turtle says he's nowhere near a thousand years old, despite having celebrated his thousandth birthday in DBZ, following the Garlic Jr. Saga.