I've been playing the game for a bit now, here are some of the issues I've encountered.
The big one, when I play the game windowed at my native resolution, it plays in fullscreen. When I alt tab out, every so often my pc will slow down, lock up, and finally crash with a blue screen of death. It's happened often enough to be an issue.
Another bug. I wish I'd kept savegames of these. If an alien gets a reaction shot on you when you run onto a teleporter pad, the teleporter pad will not activate, and the game will freeze.
One final one, when you have a mind controlled unit. I threw emp grenades at him to knock him out, then used a medkit on him to revive him, all in the same turn. Next turn he got back up, but a duplicate of his corpse was still underneath him. Normal view shows him as if still stunned, while an inventory view shows an exploded human NPC.
Not game breaking, but still weird to have a dead exploded clone body like that.
(If I may use this opportunity to sneak in a suggestion, how about having a zap or two with the stun rod helping a troop break out of the mind control early?)
The alt-tab crash is the most annoying one. I'm saving before every alt-tab I do now so it's not as bad, but I'd rather have it not crash at all.