These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Disappointing Last Level: 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.
Good Bad Bugs: In the fifth mission, it's possible to have the Klingon bad guy killed by a planetary Master Computer, 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.