It's certainly possible that it's a coincidence, but it does sound somewhat fishy.
Which seal did they replace, exactly? The only seals I know of are the inner door seal on the outer door seal.
If it were my car, I take the door panel off myself and have a look in there see if they left something inside (like a tool) that would've jammed the window up on its way down. I'm sure that if they did leave something in there and they found it later when doing the window repair, they would never admit it.
