Hmm, happened me few times:
1. All Shivans destroyed, pilot says "All done".
2. Command didn't respond, wingmen wonder why.
3. Suddenly some new fighters arrive, Athena bombers and (probably) invisible Lokis
4. One wingman says something like: This is not good, Alpha one I recommend go out.
5. Immediately I hit Alt-J and Red Alert mission will starting
but...
after 4. point I have only few seconds time. If I wait more seconds, maybe 10, I CAN depart from area and I got failure debriefing. Truly, happened me 3-4 times therefore I was angry. When I didn't departed huge EMP blast came and my ship got disabled.