The Red Devils’ team bus was caught up in congestion before the game that resulted in the match starting 45 minutes later than scheduled.
A section of the West Ham supporters are accused of attacking the visiting team bus and throwing missiles at it.
This was compounded by David De Gea being targeted during the game, with a bottle believed to have been thrown from the West Ham end at the Spanish custodian.
Rooney spoke about the bus incident before the game kicked off and stated that West Ham as a club should be disappointed by what happened in the lead-up to the fixture.
“It wasn’t nice,” City AM quote Rooney as saying.
“The coach got smashed up. We know it’s a big game for West Ham, a big night, but I’m sure West Ham as a club will be disappointed with what the fans have done.”
The FA have released a statement condemning the supposed actions and as such there could well be retrospective repercussions for the London club to deal with if it is adjudged that the home faithful were at fault.