Ferguson questioned Wiley's fitness after United's 2-2 draw with Sunderland and his comments have led to an investigation from the FA.
"I think Sir Alex may have overstepped the line this time and he may be about to get his comeuppance," Winters told the Guardian. "I think referees will be so incensed about this that Sir Alex may find that United no longer get the benefit of the doubt on certain decisions."
Winter believes the criticism of Wiley was designed to deflect attention from United's poor performance but that it will have long-term consequences for the rest of the referee's career.
"It was a cowardly attack - Sir Alex wouldn't have said it to Alan Wiley's face," said Winter.
"Every game Alan Wiley takes charge of now where he makes a decision which upsets some fans is going to result in chants of 'You're not fit to referee', he's going to be known as the 'unfit ref'. Sir Alex won't care though. He's a knight of the realm and he thinks he's untouchable, bullet proof.
"But he's also a bully. He spoke at Sir Bobby Robson's memorial service a couple of weeks ago and said he'd learnt a lot from Sir Bobby. But he hadn't, they were totally different, Sir Bobby was a gentleman. He was humble and had respect for people."