* DisappointingLastLevel: The final mission in the release version gives you a two-room mission on the USS ''Republic'', followed by a ludicrously hard fight with a Vardaine copy of the ''Enterprise''. The CD version expands this to a much bigger mission on the ''Republic''.
* GoodBadBugs: In the fifth mission, it's possible to have the Klingon bad guy killed by a planetary MasterComputer, then act like a jerk toward his subordinate, leading to a battle between the ''Enterprise'' and a Klingon ship. After winning the battle, Spock reports Kirk's actions to Starfleet Command -- but in an apparent oversight by the developers, this won't result in any reduction to the mission score, giving the impression that Starfleet are actually quite happy to have their captains going around starting fights with the Klingons.
* TheProblemWithLicensedGames: [[SugarWiki/NoProblemWithLicensedGames Solidly averted]] - it's considered one of the best ''Franchise/StarTrek'' games produced, and remains very faithful to the original series.