Plot hole: When the DigiDestined return to the real world, Izzy states that only a few minutes have passed by despite the weeks that have elapsed in the DigiWorld. However, in an earlier episode, Tai returns to the real world for hours and upon his return to the DigiWorld, only a few weeks have passed by.
Plot hole: In each episode, Emmy, and Max travel to dragon land (often for a long time) without their parents ever knowing. This makes no sense. Their parents would notice sooner, or later that Max, and Emmy always go in, and out of the house, or that it's always quiet in Emmy, and Max's playroom. You'd think Emmy, and Max's parents would get suspicious, and would question their children accordingly.
Smoking Gun - S1-E2
Plot hole: Lori managed to get to the bunker through the elevator because the modern board was still replaced by the antique one. But that implies that she was able to call the elevator as normal. And if people can just call the elevator back but the normal control board has been replaced, then they wouldn't be able to use the elevator as normal, creating quite a problem in a huge hotel. Sydney earlier was not able to switch the board back to the normal one since she went out from a (mysterious?) exit/entrance, so this situation makes no sense.