- When training a Capital Ship crew, all experience (xp) gained between the previous level and the level being trained is lost. For example: the ship is level 2 (500/500 xp) and then kills a frigate worth 30 XP. Then, when you train it to get to level 3, you end up with 1000/1000 xp, instead of 1030/1000 xp. Quite a waste when the ship is in training while it enters a fight in which it gains a lot of xp.
The training is cheaper if you already have progress towards the next level, IIRC. Obviously that can't account for XP gained during the training, but then, who's going to be doing training exercises mid-battle?

- When I save and load a game, the game settings (speeds, fixed teams, etc.) are not always the ones I specified when I first started that game. Sometimes I have to set them up again.
Known bug in 1.03, already fixed for 1.04 and to be released soon.
- Some Capital Ship abilities, such as Microphasing Aura and Missile Battery, do not seem to progress as they move up in level. Either this needs to be fixed or the progression of the ability should be described clearly in the skill description.
With Missile Battery specifically, the batteries themselves improve with each level, while the ability itself (cost, cooldown, etc) remains unchanged.
- The new version of Sins is compatible with older save files.
Unfortunately with balance changes and gameplay tweaks, that's not generally possible. Making it so would require a complete rewrite of the save format to include all of the game data, and even then it wouldn't be guaranteed.