This seems to be a very sporadic bug. Sometimes when I have more repair points than damage, I'll repair everything and then have to click the "skip repair" button that appears where the "end turn" button usually is, but sometimes I don't. The problem is sometimes I'll be rushing through my allocation and go to click "skip repair", and it will disappear on its own right before I click. Which means, of course, that I've just clicked "end turn" without having had a chance to actually allocate. I'm not sure what causes it to happen on any given turn. It seems to happen only when I've got multiple types of damage (hull + crew, for instance), but I haven't seen it enough to really tell.