If you want to continue trying to do it, make sure you go to an unvisited store with 1 health and that you don't take damage in the store location. It seems inconsistent (it will still work even in those situations sometimes), but to make things more sure fire then it'd be best to do that.
It will be fixed when I have time to push out an update.
Matthew Davis, Subset Games Developer - If you're looking for tech support, you'll get help faster emailing directly, contact info here
Since zasdarq didn't mention it: It also seems that you HAVE to use "repair all", repeatedly clicking for 1 repair doesn't count even if you end up with full hull.
This can obviously screw you if you happen to get to one hull helping a civilian who then repairs your hull as thanks :/