Funny thing is, only the cpu does that and i cannot move my units into dark space, but they can actually go by themselves into dark space.

I've seen it happen, but only rarely and minorly, with my own units on their own movements.

^That generally effects fighters being spawned far outside grav wells.

Ships that fly way out of the grav well on thier own is generally caused by fighter movement. Ships using fighter movement want to create a set distance between them and thier enemy before they'll turn around to attack. When a ship is being chased it can't create the needed distance to attack so it just keeps flying straight forever.

However, with this issue that doesn't seem to be the case. The grav well radius could be a source, but many mods have used expanded grav wells so it doesn't seem very likely. What version of sins are you using, Shuazoid?