United won the match 2-0, after goals by Wes Brown and Wayne Rooney.
Ince reckons Brown’s goal was a foul on keeper Jason Brown by Nemanja Vidic.
“I’m very disappointed,” Ince told Setanta Sports after the game.
“Whether it changed the pattern of the game, who knows? But at the end of the day, we’re still in it at 0-0. The referee or the linesman has got to make a decision.
“I went to a meeting before the start of the season with (referee chief) Keith Hackett and he’s telling me these referees are a lot fitter now and they can get themselves into position quicker.
“Obviously that’s not the case, looking at that because that’s a disgrace.”
Ince continued: “We were in the game and Matt Derbyshire had a great chance which the keeper saved.
“But once we conceded the first goal, which shouldn’t have been allowed, it was backs to the walls to be fair.
“They’re a class outfit and aren’t champions of Europe for nothing. They cut us open at times. Saying that when they can bring Carlos Tevez off the bench, who probably costs more than my first XI out there today, then you expect it’s going to be a very tough game.
“In that time they could have had four or five, which would have been a bit harsh on us, to be fair.”