"He was booed on the course and a spectator threw urine at him. I didn't see it but you could smell it on his jersey. You could think Mark was angry, but he was actually disappointed," team manager Patrick Lefevere said.
German Marcel Kittel claimed his third victory on this year's Tour de France when he pipped Mark Cavendish on the line to take the 12th stage on Thursday.
Mark Cavendish's Tour de France campaign suffered another setback on Tuesday when the Briton had to settle for third in a sprint after being involved in a crash in a chaotic stage 10 finale won by Marcel Kittel.