I know how you feel. It's actually the only big gripe I have with the game so far. I actually don't want to do too many side quests or exploration because most of the main quests are a few levels below me now. I found levelling was way too quick when I hit Velen.
Yes, happened to me too, and sounds like the exact ship. I needed to reload. I also had the same problem when I got into an old tower I wasn't supposed to, and got stuck underneath.
I really hope this guy is trolling. If not, you really don't have the slightest clue about game development or the amount of effort put into this gargantuan game.
When you right click on the repair kit, don't you have to then left click on the item to repair then hit E? I'm not in game at the moment but will take a look.