Revealing mistake: When the bridge is exploding from the mine attack, the stuntman playing Jason obviously launches himself out of the captain's chair.
Revealing mistake: When Saris is torturing the Thermian commander, he stops and approaches Commander Taggart; while Saris is talking to Taggart you can see the lips and teeth of actor Robin Sachs behind the mask.
Revealing mistake: When General Roth is threatening Jason with his claws wrapped around Jason's throat, the very moment he tilts his chin back, you can see the actor's open mouth and teeth visible inside, though he's supposed to be an alien enemy.
Answer: There didn't seem to be any special f/x that were in the trailer that weren't included in the film itself. The only shots that were certainly not in the film was the opening shot that shows the aliens watching one of the Galaxy quest shows and when the narrator introduces Sigourney Weaver where she is showing off her chest (which is a deleted scene on the DVD). Your explanation of why they are not there is the most likely reason they were cut.
Lummie ★