Missiles you haven't paid for can be equipped through auto-reload dialogue.
If you try to equip anything from a store you get a message saying that you should pay for it first.
But it looks like reloading your ammo from the quick reload dialogue doesn't make this check.
e.g.
"The arrow (+0, 1d6) doesn't hit anything. Out of ammunition.
Reload with the bundle of 17 arrows (-1, 1d6) (unpaid, 68gp)?"
The shopkeeper won't let me out of the store with the arrows equipped, but he doesn't care if I fire them and they disappear afterwards.
It's easy to reproduce if you have a bow and Barnabas is selling ammo for it.