I never heard of that happening unless you used a really harsh cleaner.

Do you have your windows tinted? If you do, your supposed to only use the GENTLEST of cleaners, otherwise that could definately happen.

If none of these two scenarios fit, I'd see if the dealer could replace the window under warranty. It shouldnt scour just using regular glass cleaner. Use your fingers and feel whether the glass is rougher there, could mean it was eaten away. I've never heard of glass "staining".