I conscripted all available people to fight the invaders and kept them at a standstill until I could gather a fleet and drove them off but at great cost. Now my own fleet has been driven away and the enemy has come back. The system management scan shows it's without troops...

Where did these come from?!

If your fleet arrives in orbit during a ground battle, they will drop their manpower in support of the ongoing invasion/defense. I suspect that is where the extra manpower came from.

That makes sense and that's what I thought at first but I am pretty sure that the "0 troops" indicator stayed that way even a turn or so after my troops dropped. Will check to see if it recurs.