I was testing out repair costs, so I botted until my Rune was at ~50% then docked. I couldn't remember if I had fired flares or not (I hadn't), so I checked my reload cost.

http://homepage.mac.com/awfwal/dump0046.jpg

I laughed, took a deep breath, and hit 'fill Weapon'. ('Re' was cutoff)

http://homepage.mac.com/awfwal/dump0047.jpg

Despite the alarming message, it repaired my ship and charged the correct amount to do so.
Why 'Refill Weapon' repaired the ship is also puzzling.

Ok, I think I know why that's happening.