During Austin's escape from the exploding boat at the start of the film, footage of the pursuing boats changes from day to night in-between shots several times.
About the 38 minute 49 second mark of part two, Steve Austin is confined by the bad guys to a small room, and chained to a table. Using his bionics, he breaks the chains, gets up and moves to the door. The hinges are on the right side of the door and the right hand wall is about one foot away from the door facing. He carefully removes the hinge pins, then, instead of swinging it open, or it falling toward him, he slides the door to the right for the full width of the door as if it was a pocket door or sliding glass door. He is in one room at the beginning of the scene and another room at the end.
In part 1, when a helicopter is coming to the submarine to pick up Steve after he is injured, one shot shows a black helicopter with no wheels while most of the shots show a light blue one with wheels.
A blue helicopter is shown bringing Donner to the sub, yet in the subsequent shots of him being airdropped, the helicopter is black and of much different configuration.
The scenes of Steve's examination and repairs are obviously just re-used footage of Steve's original bionic surgery; he didn't need his eye bandaged again or the tube in his nose because those parts weren't damaged during his escape from the villain's boat.
At the end, when Steve has carried Katrina away from Findletter's base, to a "safe" distance, they get down on the grass to watch the exploding Polaris missile destroy the base. They look straight at an ATOMIC blast with no ill effects, as the closing credits roll.
Rocket launch-tower framework and outdoor-type daylight visible in the shot that is supposedly of the indoor missile's engine being ignited. Obviously reused footage of a NASA rocket launch, enlarged and turned sideways.