The reigning English Premier League champions fell behind in the 10th minute at Craven Cottage on Saturday when Mladen Petric converted from the penalty spot.
 
But Mancini was unhappy with the decision to award the penalty after it appeared Pablo Zabaleta had brought down John Arne Riise outside the area.
 
"For me it wasn't a penalty," Mancini said.
 
"It was outside and wasn't a penalty but we're going through an unlucky moment where not many decisions have been going for us."
 
Sergio Aguero cancelled out Petric's opener just before half-time and substitute Edin Dzeko struck the winner on 87 minutes.
 
Mancini felt his team were worthy of the three points, which saw them remain undefeated and four points adrift of league leaders Chelsea.
 
"We have been unlucky for two or three weeks when we deserved to win and today we had a lot of possession and a lot of chances to score," he said.
 
"We played well and I'm happy about that. If we had lost I could say it was a bad moment but we wanted this victory and we won."
 
Dzeko's winner came after a poor clearance from Riise fell into his path inside the area, and Fulham manager Martin Jol said the Norwegian would have been disappointed with his effort.
 
"It was a mistimed ball (from Gael Clichy). I would hit it with my right foot instead of trying to head it. It was a bad clearance," Jol said.
 
"I think he will be disappointed because the mistake he made they punished.
 
"They are a very good team but there is always a possibility against them to play your football like, for example, Arsenal did last week."