FTL is, overall, a pretty well-wrought game, but there are a few small issues I have.
If you accept another ship's surrender, all of your shots miss them, even beams halfway finished. By some strange twist of fate, enemy shots have the same chance of hitting you, and that's just plain unfair - why should I keep taking damage from an enemy I've already bested? Additionally, if you destroy the enemy ship, their boarding parties keep attacking you. There's no choice to do anything except kill them, which is really a shame. It's also unfortunate that you can't do anything useful with any boarding drones left behind, but those are more wasted potential than flaws in the game.