Continuity mistake: When David and Saavik approach Spock's tube on Genesis, you can see quite a bit of dirt covering the words' red lettering, but when it does another shot of the lettering, it is noticeably cleaner. (00:30:25)
Continuity mistake: In the scene early in the movie where Kirk is talking to Sarek the guns on the wall are suddenly rearranged. (00:23:50 - 00:24:45)
Revealing mistake: When the Enterprise explodes, some of the debris briefly turns transparent. (01:12:15)