Earlier this week, the Manchester City football development executive told the BBC that he felt the Red Devils had more refereeing decisions go their way than other clubs.
City later asked that the article be withdrawn, insisting Vieira's comments were taken out of context, and the journalist who acquired the quotes was banned from media activities at the club.
"I'm trying to analyse that," said Ferguson.
"I am not sure. I mean, he's more or less saying all the referees have been wrong this season and, being an official, you are not supposed to discuss referees.
"We can bring [Roy] Keane back if he wants and make it interesting. Apparently he's retracted it a bit but it's interesting.
"The thing is, from the referee [Michael Oliver]'s position, I can see why he didn't give a penalty when Danny Murphy was brought down.”
Ferguson admitted that City had been the more impressive team earlier in the season but felt claims that they deserve the title were incorrect.
"They were playing great football in the first half of the season," said Ferguson.
"Everyone recognised that and we felt the brunt of it too when they beat us 6-1 here. But a season lasts for a bit longer than three months."
As United prepare to face relegation-threatened Blackburn at Ewood Park on Monday night, Ferguson also paid tribute to Rovers manager Steve Kean.
"I am sure a lot of them are saying to themselves 'I wish I hadn't done that'," Ferguson said, of the Blackburn fans who had harshly criticised Kean during a poor run at the start of the season.
"Now no one is talking about fans having protest marches. He has held his dignity very well and deserves 100 per cent praise from everyone, including his own supporters.
"He has shown his mettle in times when it was difficult for him."
Ferguson went on to suggest that even though he will have a full week's preparation between Premier League games during the crucial run-in, he would still rather be in European competition.
"We have been used to playing midweek games for so long that you do miss it," said the United boss.
"The players miss it too. Yes, we do get freshness but you can't have it all ways. We would rather be in the Champions League."
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