You must be running one of the super mods, I've heard of that million destroyer bug but never saw it.
As for the phantom reappearing ship bug, I haven't seen it in a while, but I'm pretty sure it's somewhere in the mission file. I used the mission editor to hack EastAsiaCampaign.mis in particular, because that one was the cause of all those screwy invasion forces with the teeny troopships forgetting where they were going and chasing each other around in random stop-start circles.
Some of the other campaign missions might have the same sort of problem, but that one was infested. The reappearing targets that you sink twice with no credit for the second one may be related to the "delete on final waypoint" check, haven't been able to positively either confirm or disprove that.