Following Ashkan Dejagah's opening goal, the Magpies had their claims for a late penalty turned down by referee Howard Webb, after Tim Krul's shot appeared to hit the arm of Johnny Heitinga.
Carver believes they were denied a clear penalty and was disappointed to leave Craven Cottage empty-handed.
"I've just had a look at it - and it hits his arm," he told Sky Sports.
"There's no pace on the ball so it's not like it has happened quickly.
"I've spoken to Howard and he says he was in a difficult position to see it so he hasn't given it. We have to accept it."
Carver, who was standing in for the suspended Alan Pardew, believes that Webb missed a foul on striker Luuk De Jong moments before Dejagah's strike.
"I'm a little bit disappointed with the decision about the challenge on Luuk De Jong that led to their goal," he said.
"Again, it's something I've just looked at and he goes straight into the back of him - you wouldn't get away with that on a Sunday morning."
The Magpies' assistant admitted that his side defended poorly for Fulham's goal, believing Krul could have "possibly" saved it.
"What we should have done is defend a little bit better," he said.
"He comes inside on his right foot and we shouldn't open up the goal - he should go on the outside.
"We warned Mapou (Yanga-Mbiwa) how to deal with it, and we didn't deal with it."