A couple of 'bugs' or rather something more mild - loose ties/exploits/inconveniences.
1. Apoc equipment system.
When you equip people from base's Soldiers screen, IF a soldier is onboard craft, the game fails to move the equipment you have just given to that soldier onboard craft, therefore your changes are not put in effect. Therefore you're forced to take all the crew off the ships, which is a lot of extra clicking...
2. Craft equipment giving +HP/-HP
Currently there is a rather ugly exploit. First off, when +HP equipment is installed, the craft needs to repair up to new max HP. This is not a huge problem BUT: when it repairs fully, and you remove the system, ship's HP stays at new level (>100%). -HP systems surely have related issues...
My proposition of an easy to understand and I think foolproof solution: when equipping or unequipping +HP/-HP system, ship's HP percentage is unchanged, and the actual number of HP is recalculated. This avoids the mentioned issue, also avoids having the ship reach 0 HP due to unequipping +HP item or equipping -HP item.