I now that the game has a limit to how much actors/weapons that can be "alive".

Not sure if this is part of the problem but I have a nagging suspicion that it does.

Details:

I played R.E.T.A.R.D.S skirmish on the nanobot bunker map. I used Phoenix copters, and the Space Marines mod. After a while, I started to notice that there were random metal entry/exit wounds moving in midair. After a while, my whole base disappeared.

Yeah, you were using too many bunker modules for CC to handle.
Presets are pretty handy in this case.

Bah humbug. I just wish the scene editor was easier to use, then I wouldn't have to deal with setting bunkers in-game.