Continuity mistake: In the one scene in Dr. Evil's evil headquarters, it shows the large screen opening in front of them. The screen shows the warhead that they're going to arm the drill with. The table in the room is reflective, it shows the panels of the screen opening, but it does not show the image that's on the screen reflected in the table.
Continuity mistake: Towards the end of the movie Dr. Evil is talking to Austin in his evil headquarters. Dr. Evil is sitting in a chair with Mr. Biggelsworth in his arms. The scene has close ups of Dr. Evil with a sleeping cat, and broad shots of Austin and Dr. Evil, with the cat trying to get away. It keeps switching from one shot to the other.
Continuity mistake: When the security guard comes back with the orange sherbet, he hands it to Austin who takes it from him. But a few seconds later, when Austin and Vanessa are escaping from the destructing lair, neither Austin or Vanessa have the sherbet with them. [Just a note regarding this scene, the international version of the film contains this scene but not the US version. I believe it is a deleted scene on the US version of the DVD.]
Continuity mistake: This mistake takes place when Austin, Vanessa, and the guard are with the mutated sea bass. When Austin judo chops the tooth paste onto the guards face, the guard is wearing a helmet and half of it has toothpaste on the front. Then the camera does a close up on Austin. When it shows the guard again, he doesn't have his helmet on and half of his forehead has toothpaste instead of his helmet.
Continuity mistake: Watch the distance between Austin and Basil Exposition just as their first meeting comes to a close. It changes from far to near and back to far in the space of a couple of shots!