United had to settle for a 1-1 draw after Zlatan Ibrahimovic saw a 71st-minute equaliser ruled out for offside, but replays suggested he was onside before he headed the ball past Everton goalkeeper Joel Robles.
'Ibra' eventually did level the scores in stoppage-time with a penalty to cancel out Phil Jagielka’s 22nd-minute opener, but Mourinho said the Red Devils had been unfairly denied victory.
“With the VAR (video assistant referee), we win this game 2-1 because it’s not an offside,” Mourinho said.
“But it’s a difficult one for the linesman. I’m not critical of the linesman. I just say when the VAR comes, it will help everyone, especially the linesmen and referees.”
Ibrahimovic also thought he had scored, adding: "I thought it was goal because I came from the right side of the defender when he played back and I thought it was a goal. But I cannot say, the TV has to judge.
"But at the end we equalised, we were attacking for most of the game and we had good chances – we hit the post one time I think – but we have to do more."
The big Swede lamented Everton's goal, and said United could not afford to lose focus as they slipped to another draw.
"I think we deserved a little bit more. I mean we conceded a goal by mistake, the first mistake by missing Williams I think [it was who] headed it and then the goal came out of nothing," he said.
"We need to keep focus, we cannot afford these mistakes, especially now in the end [of the season] because it's very important points especially when the table is like it is. We are close, but still we don't get the points that we need.”