Lisandro Martinez scored a deflected goal late in the second half, which was United's only shot on target at Craven Cottage.
Silva felt the result was unfair given Fulham's overall performance in the contest.
"I think it was cruel for us tonight," said Silva.
"The result, their first shot on (target) on 78 minutes, I think clearly we were the team that had more control.
"Our pressure was really good first half, we created enough chances probably to score a goal in the during the first half.
"We didn't give anything for them. I don't remember one dangerous moment from them during the first half.
"Our second half was not as good. Unfortunately for us, a really lucky goal, deflection, they scored.
"After was the reaction from ourselves. They came with a low block, they had players around the box. We had a great chance with (Joachim) Andersen from a corner.
"I think the result is really unfair for us, it is not what we deserve from the game, but football is like that. The margins always play a big part in it, and they are very lucky to win tonight.
"They tried to press in some moments but we were always able to make the ball arrive to (Saša) Lukić, Emile (Smith Rowe) or Sander (Berge). I think we had superiority in that area of the pitch, I think we did really well.
"Of course, wasn't the best night from us in our attacking line at all. I think we had some very good moments that we should have taken more from and created even more clear chances. Definitely, in terms of our counter-attack, was not the best night at all."