How can you be sure it wasn't, it's all about probability, you clean the insides and the insides are now damaged, you can look and make your own mind up whether this customer scratched them or not, had scratches been there before you cleaned the glass this should have been noted and shown to the customer.
Tread carefully, because any reluctance on your part may very well come across as saying the customer is a liar, remember there are two sides to every story - then there's the truth !!
Please don't go down the you can't prove it road.. It's all about probability, if you want to keep the customer then pay up, you'll soon recoup the cost by keeping the customer, or put two fingers up, walk away, and lose a customer, have a dirty mark on your reputation, and not resolved the problem of why a worker scratched the glass.
This crops up from time to time, it happens, been there, done it ( well staff have ) use this experience to improve your t's and c's with staff and their training and customer relations
Darran