I noticed that for some abilities if you click on it a certain way it will keep using the ability when the cool down expires until it no longer is able to use it (i.e. out of antimatter), that may be the cause of this.

This is only a suspicion but I think it automatically drops turrets when it's being attacked, even if by strikecraft (which the turrets obviously can't hit) - it might also drop them right after warping from a well with an enemy starbase due to the hull damage caused.

Or did you see it happening in other cases as well?

I can't reproduce this.

You don't have the auto-record saved? That'd save you a lot of play-time.