Continuity mistake: Briareos' VTOL fires all of its forward missiles twice. (The forward missile bays have distinct markings in the form of a set of three white rectangles at each side). (01:15:26 - 01:16:40)
Plot hole: The main plot of the film involves Iris and Olson's mission: Destroying the Mobile Fortress 000. But Iris is a special gynoid. Her primary function is to activate the Mobile Fortress. The antagonist of this film could unleash calamity if he had Iris and the fortress. So, which idiot has sent Iris on this mission? The logical course was to send a demolition team, or better yet, send no-one at all. Anything is better than sending the activation key outside the safety of the Olympus.
Character mistake: Olson discovers a "microchip blocking the self-assessment program" and says, "it's a worm"! It is not. "Computer worm" is a type of malware that propagates over a computer network. What Olson discovers is an act of sabotage of malicious nature, but definitely not a worm. (00:25:39)
Continuity mistake: When Talos enters Two-Horn's room, he doesn't have a pistol. A minute later, he does. (00:31:04 - 00:32:00)