Funnily enough, the little things are what really add to games. Freespace did a pretty good job at this, though it's probably mainly because I don't know too much about the topic to be annoyed by incorrect little things. The star thing with Cappella could be hastily rationalized by saying that you're positioned so you can only see X amount of stars at one time. Very unlikely, but it's still a possibility. Similarly, little things can ruin games, too. Take MW2, for example. ACOG sights do not run electricity; they would not go dark like they did. Privates are not put in charge of half squads, especially when a corporal is included in that half squad.
I think part of the difference here is that any major inconsistencies in FS would be rooted in FS's universe, and thus somewhat justifiable if you elaborate on the universe enough. Still, it's not good to have to do that, as I'm sure many of you are aware, and I am so painfully aware myself. MW2, however, takes place still in a different universe, but one MUCH more similar to modern day, and thus the little things stick out much more.
Still, little things are what they seem: little things. They're annoying and they really detract or add from or to the game, but they don't break or make the game. A game that I'm quite confident that did this in a stellar manner is Deus Ex. Everything is so thorough; for nearly whatever the player does, there is a reasonable consequence for it. The same can be said for Freespace I feel, but with much less persistence between missions. Even within missions, it doesn't quite match up to Deus Ex, but then again, not much does in these regards.
tl;dr little things are like bonus points for developers.