i take the attitude now that it was not us that scratched the windows. it would have to be something very obvious, that made sense with how we clean the windows for it to be us.
if they have had recent building work, or if there had been building work next door that caused it (from concrete splashes or cladding) then we take the attitude that the glass is damaged when the concrete hits it. it is not us cleaning any of the concrete off that has damaged it.
we had one last year which was like this, the most likely explanation was that there was concrete on the windows from an extension next door, and when we cleaned did our regular clean and cleaned the splashes off the glass was scratched. i paid for the glass to be replaced (about £200) the customer emailed me to say how i had restored her faith in companies and how impressed she was with our service, and then within 3 months had cancelled because she had decided to clean the windows herself
if you're confident when you visit them and tell them that you just can't see how you could have possibly scratched glass with your equipment then you'll be fine. explain how you clean 100s of windows every week and how this is the first time you have had anyone suggest you scratched the glass.
good luck!