The Cottagers were impressive in the opening exchanges before Ebere Eze and Ismaila Sarr struck within four minutes before halftime. Eddie Nketiah took the game away from Fulham midway through the second-half as Palace won 3-0.
Afterwards, Silva said: "One game until 25 minutes of the match, we completely dominated and we had three or four dangerous moments around their goal. We should have scored in those moments.
"You need to be ruthless and clinical. They are solid and compact. They set nine players around their box every single time and when we are able to create, we have to score. We didn't and we were not strong in both ends this afternoon.
On Palace midfielder Adam Wharton avoiding a second yellow card, Silva added: "For me it is clear, it's a second yellow card but we are used to these kind of situations. I prefer to say we are unlucky but it has been a long story with us.
"Of course VAR cannot overturn this decision but you have many eyes inside the pitch, the linesman has all the angles to see it, the fourth official. It is a clear second yellow card, definitely. It would have a massive impact on the game but against us it is always more difficult to see.
"We have been unlucky in these type of situations and let's hope it will be balanced at the end of the season."