Scraping rattle noise after recently replacing the clutch

My car was making a weird noise almost like a scrape or rattle. I assumed the clutch because it was recently replaced and the noise completely stops when the clutch peddle is pressed in. The car itself drives fine it just makes the noise louder at lower speeds. I took it back to the people that fixed the clutch, after a week they finally dropped the transmission and are now telling me I need an entire new transmission. When I asked what was wrong with it they said "something internal" I asked what exactly and I was told I could not be given an answer that it was just internal. They said if I want to know specifically it would be $900.00 in labor alone plus parts. Again the car was driving fine just making the noise when the clutch peddle was not pressed. Am I being cheated out of money? Or does it seem legit to you all? When the car was completely at a stop some gears did seem ruff, but when driving, it was fine.