[nelly]

I'd say if the belt covers were replaced correctly, then no. There's no way a stone would get in.
The only way I can see of it getting in is either one of the covers wasn't on correctly, or as you say, it fell in there when the belts were replaced.
This is easily done if it's sat on/near the cover, maybe even held there with a bit of road tar etc.
I'd have a word. You're right, you shouldn't be paying for this. See what their reaction is. If they get ****y over it then make it more formal??