TMP - The tiresome stalling which was obviously designed to stretch a one hour episode to feature film length.
TWOK - Khan's anger towards Kirk for not checking up on him on Ceti Alpha V. "Space Speed" contained absolutely no promise from Kirk, or any demand from Khan, that anything of the sort be done.
TSFS - The return of Spock, which made the death of Spock in the previous movie utterly pointless
TVH - Why didn't they replicate something more low-key for Spock to wear than a white robe?
TFF - The whole movie
TUC - The Scooby Doo ending.
GEN - Picard's decision to go back to Veridian III with Kirk to stop Soren, when he could have simply gone back to Ten-Forward and phasered Soren right there before he destroyed Armagosa.
FC - The Borg's decision to try and invade the Federation with only one cube when it clearly didn't work before.
INS - Why the entire "smuggle the Baku off the planet" thing was considered when it would have been obvious to them eventually that they had been moved. It would have made more sense to simply beam down openly, explain the situation to them, and move them, since legally the Baku planet was in Federation space.
NEM - The whole movie.