Security believed the fans were about to engage in a green and gold protest and refused fans entry.
Green and gold scarves have become a visual reminder of the opposition to the Glazer family's ownership of the Red Devils at United matches since January.
Supporters groups opposed to the Glazer regime estimate that "99%" of fans are against the owners, who they hope will accept an offer for the club from the Red Knights group which is due to be launched at some point in June.
Both Sir Alex Ferguson and United chief executive David Gill have backed the rights of fans to protest, even if they do not agree with the sentiments.
Only this weekend, Gill addressed the issue in the Manchester United Disabled Supporters Association magazine 'Rollin' Reds'.
He said: "I have asked the players and they say they are not distracted, but if your question is 'would I prefer all red and white instead of gold and green when you have a full stadium and you are playing host to famous opposition', of course I would.
"If the question is 'would I prefer not to look out of my office and see the scarves they are selling on the street', of course I'd prefer that. But as Alex has said, people have a right to protest.
"Nobody is going to stop that, and in the ground itself we are not going to stop that."
However, United's security experts CES today stand accused of ignoring that stance by the Independent Manchester United Supporters Association.
"The reserves played Aston Villa in front of a crowd of about 4,000 but many fans were prevented from seeing their victory as large groups of CES (who were again not showing their badges) stopped people in their twos and threes from gaining entry because of their supposed involvement in protests on other occasions," said a statement from IMUSA.
"We are also told that the local police intelligence officer joined in with this intimidation, giving people 'verbal warnings' for having engaged in legitimate peaceful protests at other matches. This same officer told whoever cared to listen that 'he didn't need a reason' when asked why he was evicting a small number of young teenagers from the ground.
"IMUSA remains deeply concerned about the moral and legal implications surrounding this heavy handed approach to the suppression of legitimate protest."
United are currently gathering details of yesterday's events before deciding their response.