I'm not sure how significant this bug is because I haven't had actual damage to repair.
By Habit whenever I dock I hit both refuel and repair. I noticed that when I hit repair I get the message "repair failed. you don't have enough money" despite having plenty of money. This might only be a bug when the repair failed because there is nothing to repair and the message gets mixed up or it might be that repair always fails. Not sure.
-Loudent