Eww.. that's pretty bad . I'm glad I've always done repairs manually and chosen how much to pay.. I can surely see somebody not paying attention and getting reamed by that one.
It would have been an interesting experiment if you had scrolled the repair slider down, until the cost of repair was just slightly over the real cost. (say 9 peds v's the 7.47peds required to fully repair.)
Then repair the gun, and see if you got charged 9 peds, or if in fact you only paid 7.47. (or ended up with a gun worth 61.5 peds out of 60 )
it would only be a problem if you paid 9, but got 7.47 peds of repair.