Hi! In the mission where you need to destroy the transports landing on Antares Station and then the escape pods fly out, one of the escape pods is flagged to not be destroyed, but its engines can be destroyed - and I have, multiple times, on several repeats of the mission (destroyed as soon as it flags hostile, caught up to it with burners, ai just flew to it and blasted it.) Once destroyed, the mission basically freezes in place, since everyone gangs up on it and it never moves again, but it's never destroyed.
Also, in How The West Was Lost (the strikebusting one), the checkpoint puts you 35 kilometers from the action. The Return to Base directive also shows up significantly before the entire convoy is in, and even if you wait until Protect Convoy is completed, you get chewed out by command for having ships fail to get through - even when none were destroyed.