Hmm. I seem to recall a problem in earlier builds whereby if you had a station targeted through the Nav panel, but also had another ship targeted through the target selection bindings, it would prevent the Safe Disengage feature from working even if the speed and distance were correct. You'd shoot past the Nav target and drop out at a very long distance if you pressed the SC exit button.
I thought this had been fixed but it sounds very similar to what the OP describes. Maybe the bug is still there (or came back) and I don't see it because I got used to deselecting weapons targets when approaching a Nav target. I'm not able to test the game right now but I'll give it a go when I'm next at the PC, unless someone can verify or refute this theory in the meantime.
But AFAIK, stations are static pois, while missions are not, if you fail disengaging the FSD in the signal, it just vanishes as if you drop of supercruise to normal space. Stations however, as they are persistent would still be there.