I've been playing Empire at War for a year now, and have been playing Forces of Corruption for a somewhat shorter time. Here are the bugs I've noticed with FoC, and this is using the latest patch:
* Forces of Corruption seems to have a bug where my fleets will randomly disappear. I will create a massive fleet of varying types of ships, go around the map, and come back to the planet and find it empty. No battles, no notice, nothing. The fleet's just gone.
* I've encountered a variation on this bug when choosing to battle an enemy fleet that the game considers to have "left" the battle when you arrive. All of a sudden, it will say I've lost huge groups of fighters, from when the enemy never even fought! Weird.
* This is an Autoresolve issue: As everyone knows by now, if you destroy an invading space fleet, there will be another battle immediately following, of all the ground assault shuttles that arrive afterwards. If I "play" the battle, I destroy all the shuttles. But if I choose to Autoresolve, those shuttles somehow destroy a few capital ships! That's ridiculous, and I've even seen it with only one enemy shuttle.
* Autoresolve itself is a joke. It in no way reflects reality. I really think it's just a random number generator, although you generally will always lose unless you have a massive pile-on of ships/ground troops.
* Finally, as others have noted, not playing the corrupt side means you'll pretty much lose. The only possible strategy is to never spend a penny ridding worlds of corruption, and just trying to make gains in military battles. You'll go bankrupt curing corruptions, and never have money for even one ship! Playing as the Empire on medium setting, I was shocked to see 6 worlds corrupting at once. That is ridiculous, and shows the computer is cheating, when no player would have that much money at once.
And that's the biggest problem of all with the expansion. Some nice possibilities overall, but when the AI is obviously cheating, you've lost my interest as a player. Too bad, as the game had promise.