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The Football Association is to launch an investigation into the incidents before and during West Ham's final game at Upton Park on Tuesday night.
Kick-off was delayed by 45 minutes after the Manchester United team bus damaged as it made its way to the ground with a window on the bus smashed as objects were thrown from the crowd.
Items were also thrown inside the stadium and the FA has confirmed it will carry out a full investigation.
"The FA strongly condemns the unsavoury incidents this evening involving both the Manchester United team coach outside West Ham United's Boleyn Ground and objects thrown from a section of the home support during the game." a statement from the governing body read.
"We will work closely with both clubs and the Metropolitan Police to fully investigate these matters."
Speaking immediately in the wake of the incident, West Ham co-chairman David Sullivan suggested United should have arrived at the ground earlier but the club has promised to issue lifetime bans to fans involved in the attack.
"It was an extraordinary night full of extraordinary moments in front of extraordinary fans. 99 percent of whom behaved impeccably and were a credit to the Club," a club statement read.
"We have already had thousands of tweets and emails from fans to say how proud they were to be a part of such a special evening in West Ham's history.
"However, we are aware that there were some supporters outside the Boleyn Ground who didn't act in an appropriate way when the Manchester United team bus was damaged.
"That was not acceptable and we will work with the police to identify those responsible and ban them for life."