I'm going to keep this as short as I can.
1. Game pretty much always crashes if you want to view combat, and the AI initiated the combat.
2. AI, on all difficulties for me, only goes around with single ships. Never seen a fleet, except for pirates.... they sometimes build weak fleets. And no its not because they haven't researched logistics, have confirmed that they had it and this was hours into the game.
3. There is something massively wrong with the Altarian race. I could have everything to counter their ships, custom race accuracy +2, do everything I can support wise to increase accuracy, and one of their ships will take down my entire fleet. A SINGLE SHIP, with pretty much no defenses that is outgunned by only one of my ships (I'll have an entire fleet going after it)... and yet I somehow miss with an entire fleet and every 100th time may hit them. To destroy one of their ships that should lose to only one of my ships in 1v1 combat... it takes me 4 solid fleets to take down ONE of their ships. (probably the most irritating bug I've encountered, the crashing to me is less annoying). I've observed this bug on literally every single game I've played.
4. The diplomacy is bugged. As in, I can be close to someone with many more -'s than +'s, as in I'm doing everything humanly wrong to them and they still want to be best buds with me, making it insanely easy to win by alliance. Almost seems as if the -'s aren't counting.
That's the majors bugs I've noticed thus far.