Simeone was pelted with bottles and cups as he sprinted down the touchline towards the tunnel following United's Champions League exit at the hands of the Spanish champions.
Renan Lodi's first-half goal earned Atletico a 1-0 win on the night and a 2-1 aggregate victory to book their place in the quarterfinals.
United, meanwhile, have won just two Champions League knockout ties since 2011.
UEFA's disciplinary body are awaiting reports before deciding whether sanctions are necessary.
Sources have told ESPN that United will look to identify the fans involved in throwing objects at Simeone, and those found guilty will get three-year ban from Old Trafford.
Speaking after the game, Simeone played down the incident insisting he was not aware that objects had been thrown at him from the crowd.
"When I came off the pitch, I ran because I was happy and I like to enjoy it in the dressing room," the Atletico boss said.
"So I don't know what happened. What you just said, all I was thinking about was getting into the changing room to the dressing room, and I was really happy."