Queiroz said: "How can the referee not see that Ballack has jumped on Ronaldo?
"It must be necessary for a player to bring a gun and shoot one of our men in the box for us to get a penalty."
Chelsea's dramatic victory moved them level on points with United at the top of the table, although United have a superior goal difference.
He added: "The referee was five metres away from both penalty incidents but he gives only one penalty.
"It is a hard to say what is going on with this game. I have to talk about some of the decisions in the last few weeks that have damaged this football club.
"We are not in the FA Cup final because of a bad decision when we should have had a penalty against Portsmouth.
"Against Barcelona in the Champions League on Wednesday, there should have been three penalties but only one was given.
"Something is wrong with football."
However, Queiroz insisted that United will not falter in their pursuit of the league title and says it is vital the club now supports the players after what he perceives as recent injustices.
"We have a job to do at this club and we have to win our next few games," he stated.
"It is important to support the players because after 90 minutes of effort and commitment, we want them to feel it is a fair game for them.
"The defeat by Chelsea has not caused any damage for us. We will concentrate and do our job and stay committed."