I had this problem with a different mod. I have no idea if it's work, but try the instructions down below. It's on the "New Galactic Order" thread, Shangtai told me it on page 16. It may work here if you follow it correctly.
"Yes i try sim,
And i found fix: in mods\New Galactic Order 1.06\data\campaign\sim_opponents
change (last line) ngo_experimental_phase_fighter_balanced to ngo_experimental_phase_fighter_standard"
Thanks for your suggestion. I didn't manage to get it to work, but it did make me digg a little deeper, and actually look at the error message in more detail, and I think I figured out what is wrong.
I had run into a group of hostile Imperials ships (from some bounty, I assume) while out exploring, and I manage to capture two Imperial ships from them, one Invictus and one Legionary, and both of them has permanent damages.
I returned with these ships to the 'OmniFactory', from the same named mod, and 'scanned in' these ships, before going on my merry way, to give the Factory some time to be ready to produce these lovely ships for me. Yet, when I try to actually look at these damaged ships, I get another error.
My assumption is this: The OmniFactory is trying to display a permanently-damaged ship (in this case an Invictus), but there is no 'hull variant' or 'hull spec' for permanently-damaged Imperial ships. I have tried this before, with non-damaged imperial ships, so that works. I can only assume that the Dark one never though that permanently-damaged Imperials ships would ever need to have stats in the way the OmniFactory wants it.
And this would lead, after I have flown around quite a few days, to the OmniFactory suddenly wanting those 'stats', even without me directly looking at, and that is what crashed my game. Though again, not consistently, which seems odd to me...
While I can swear that I had the first bug I spoke about even before I feed that damaged Invictus to the OmniFactory, that I can managed to replicate this second error without fail, dose seem to suggest I found where I did wrong. I guess I will just have to get these lovely ships, in a slightly more 'undamaged' condition...