Didier Drogba had an effort ruled out for offside against Eidur Gudjohnsen in the 1-1 draw against Everton at Goodison Park.
Mourinho said: "My opinion is that we scored two goals and should have won the game but I do not know why the referee disallowed it.
"Even without that goal, I thought we dominated the game and deserved to win it because we were the best team.
If the linesman is not sure of the decision he should protect the attacking team by giving them the doubt.
"But I thought in the second half we were fantastic.
"It is not easy to be losing away from home against a team who were fighting for every second of the game.
"All credit to Everton. They fought for every inch of the pitch and wanted to make this game a fight and it was a fair fight. They were aggressive but correct."