Assistant manager Steve Kean believes Bolton’s first goal should have been ruled out for a foul on Brian McBride.
The Scot was disappointed to see Dermot Gallagher not call back Bruno N’Gotty’s challenge on the big American striker prior to Stelios Giannakopoulos’s corner.
Claus Jensen received a red card for using his right arm to clear N’Gotty’s eventual downward near post header off the goal line before Trotters skipper Jay-Jay Okocha eventually scored from the penalty spot.
Kean also felt Jensen had not deliberately used his arm to clear the ball from N’Gotty’s header.
“We felt it was a foul on Brian McBride by N’Gotty first of all,” insisted Kean.
“It was a genuine attempt by Claus to clear the ball. He took it on his chest and it clipped his arm.
“We see it as ball to hand rather than hand to ball and we are disappointed at the decision.
“We hope the referee will revise his decision in the circumstances.”
Defeat for The Cottagers leaves Chris Coleman’s side just six points above the bottom three, but Kean is unconcerned by the club’s place in the table.
“We are not concerned by the situation,” he added.
“There is a good spirit among the squad and we are looking up as opposed to down and looking forward to the remaining games.”
Fulham left the Reebok Stadium with a feeling of injustice and are set to appeal against Jensen’s sending off, which leaves him facing a one-match ban.