Call and write your builder and let him know that it is not acceptable to have it just cleaned after coffee and red dirt have been spilled on it because that stuff sinks into the fibers and that you will only accept him paying to pull it up and replace it.

What the hell is wrong with people? (rhetorical) That sticky plastic stuff would cost about $100. My unkind / skeptical self thinks that your builder is trying to take advantage of your distance. THAT is what annoys me more than anything....

and agreed with cp - new carpet. NO EXCUSES - because those stains will likely come back even after it's cleaned (about 2 weeks after you move in probably... or 24 hours after the check clears if I am extra cynical)

Did your inspector send you pictures?

Why wouldn't the carpet be the last thing done?

definitely don't settle. But request pictures.