The 2-1 loss saw Jordan Ayew sent off and Palace on the wrong end of VAR decisions.
Hodgson said later: "There's a lot more than simple frustration and disappointment, sadness and being gutted about the result.
"It's really a feeling that there are a lot of things going on which are taking the game in the wrong direction at the moment, in my opinion.
"There has always been decisions in matches which affect games irrespective of whether we have one or two referees in the game.
"I would say that the thing that bothers me most is the interpretation of the handball rule, what time-wasting is, the interpretation of the danger of more than one person standing in the technical area to shout advice to the players - that annoys me a damn sight more.
"To say I'm gutted about the way that game went and the result we have had to accept today would be an incredible understatement.
"I am very disappointed. I think we were very harshly treated. Unfortunately going down to 10 men cost us. I told the referee what I thought at the end of the game. I'm not going to repeat it. He might."