Audio problem: When the 1st WSP Commander is speaking in Washington D.C. he is voiced by Don Mason, but when he speaks to Commander Shore at W.A.S.P., he has a completely different voice provided by Ray Barrett.
Continuity mistake: As the red liquid fills the tube to measure how long Troy's trial has gone on for, it changes to black halfway through.
Continuity mistake: When Troy and Phones are being transported to the Terror Fish, Troy is sitting in the left chair and Phones is sitting in the right chair. But when they are in the Terror Fish, the two of them have changed positions.
Continuity mistake: During the transformation scene in Agent X20's room, X20 walks to the control panel with a pair of binoculars in his right hand. In the next scene, the binoculars have suddenly disappeared.