Since my laptop recently decided to be able to actually play the mod(thankfully) I have noticed one thing. The only glitch that I've actually faced is that whenever I tried building a CAS class, a Plot Device class would spawn, but won't be able to build anything.
Now the balance is a bit of an issue. The covenant capital ships are severely underpowered. They get taken out with just a few macs, and they don't do enough damage fast enough to compensate for their fragility.