Bruce believes Paul Scholes was lucky not to be sent off and was also fuming over the penalty his side were denied and the one they conceded at the JJB Stadium.
"You should ask the referee about his integrity, not about my team. Thankfully there was nothing riding on it for us but I have to say three decisions in the first half were absolutely unbelievable. You would have thought Rio had gloves on and to say the penalty we conceded was harsh is an understatement."
Bruce, however, could not disguise his affection for United and Ryan Giggs in particular.
He said: "Ryan scored on his debut and has equalled the appearance record today. He is a great, great player. He epitomises what Manchester United are all about. He is an absolutely fantastic player.
"The big strength of United is their strength in depth. You look at the bench today. It is a squad that is capable of playing 65 games. That is the biggest thing going for them. Of course they have outstanding players but it is their strength that sets them apart."
Wigan gave their all on the final day, as did Bolton in claiming a draw at Chelsea, who as a result finished two points behind United.
Bruce added: "There is an honesty and integrity in this league. We have put up a hell of show and it has taken a really good team to beat us.
"Bolton have gone to Chelsea and got a draw. I don't think that would happen anywhere else around Europe."