Here is a error.txt of a multi-player game where it crashed during system assault. It did crash more than once as we reloaded the auto-save and did not seam to be related to the way you decided to attack the system. It may have had something to do an orbital battery. I am told one was there but I do not recall seeing it. This is using the 20130203 build.

it was freshly build, maybe that's been the cause

The orbital battery was brand new?

The other system assault issue is a one of design. It had to do with getting run off from an assult but not before doing some damage in a system assault situation. See what you think about this: I got three Fed Scout I ships to Qu’nos. Qu'nos belonged to the Romulan Empire. I took assault system for my next turn. On the next turn a superior Romulan force gets to Qu’nos. I take retreat and then combat took out two of the three ships. The one still retreating ship still got to assault the system doing damage and ending the turn in a square next to Qu’nos. Was that too much to expect or, given I was ready to assaulting could unload on it to the full force of my one ship while the other cover the action? Should the degree of assault be cut short or cut out all together because I took retreat?

I just managed to power that orbital, so it's been build one turn ahead
however I forgot, it didn't help you to wait one more turn either

regarding Qo'nos, not only did he manage to attack my system while retreating
that single scout I wiped quite some buildings including my only type 5 farm I needed to invest many turns to build

one other strange happening was when I build an outpost somewhere and it happened to perform the build one sector apart. But I guess I accidently ordered to move these ships while giving the build order.

another thing I noticed was when loading the autosave the turn before reported exception
while Kenneth attacked one of my systems I took omarion but while loading the autosave correctly reverted it, sectors around dominion influence of omarion were marked green. only the ones I would gain influence range but dominion has not
just a visual issue but strange, looked like a green ring around it

one further thing I dislike is the red shield bars. In any game I know shields are blue or green and hull is red. that's been a bit irritating in ship fight.

So there is a bug in orbital batteries for system assault. I wonder where we should draw the line here from 3D combat and the system assault Mike has already built?

Could you try to replicate this next game, giving a detailed description of what was done and what happened exactly, including any details that might be relevant? That could help nailing the problem.

Same thing for the assault system problem.