Supporters were gathered outside the east London stadium, which has been West Ham's home since 1904, before the last home game ahead of next season's switch to the Olympic Stadium.
Manchester United's team coach was stuck outside the car park, and captain Wayne Rooney blamed home fans for attacking it.
"The coach got smashed up but we'll just have to go and prepare and get on with our job," the England star told UK match broadcaster Sky Sports before his team's 3-2 defeat.
"I'm sure West Ham will be disappointed with their fans."
However, West Ham co-chairman David Sullivan blamed Manchester United for not turning up earlier.
"Man United should have got here at 4 p.m.," he told Sky Sports. "They know it's our last game. They had the same problem at Tottenham a few weeks ago. I think the police and officials have been kind. I'd make them kick off at 7.45 p.m. if I was in charge."
"I'm gravely disappointed, more for our supporters. What people forget is they've got trains and buses to get home and we've got a wonderful, wonderful show after the game for them. Many just can't stay any more."
Manchester United's match at Tottenham in north London last month was delayed by 30 minutes because the visiting team's bus was stuck in traffic.
The club's manager Louis van Gaal said Tuesday's incident was "not so nice."
"The way we have been received is not the proper way," the Dutchman told Sky Sports before the game kicked off.
