The Cottagers gave up a one-goal lead in the dying seconds to be held to a draw at Craven Cottage in a night full of drama, which saw Fulham's Stephen Kelly sent off for a challenge on John Arne Riise in the box.
The tackle led to him being sent off and the referee awarding Roma a penalty, which goalkeeper Mark Schwarzer saved, prompting Hodgson to question the decision that end in the end may have caused the match to be a draw.
"I've got my grave doubts as to whether it was a penalty, but they get given in those situations when a player drives into the box," Hodgson said.
"They [the extra officials] got the wrong player with the red card but they should be making it clear that you can't give that as a last-man foul when someone [Hangeland] is coming across to cover."
"They bought their best players on, and we were short of numbers and we were short for a corner - which led to them equalising with the very last kick of the game," he added.
"We had a marvellous first half - I thought we played very well. At half-time, we made some changes. But they bought on Mirko Vucinic and Claudio Pizarro, two of their better players.
"It's very difficult to play with 10 men. But I thought the effort was magnificent, and it was cruel.
"After conceding a 92nd-minute goal with 10 men against West Ham, this is very hard to take."