Steve Sidwell had given the hosts a first-half lead at Craven Cottage, before Dimitar Berbatov doubled it from the penalty spot just nine minutes later, following a contentious foul on Alexander Kacaniklic by Leandro Bacuna.
The decision to award the spot-kick angered Lambert, as did a late challenge by Aaron Hughes on Gabriel Agbonlahor inside the area, and the Scotsman was left ruing the officiating as his men remained in 10th place
"I don't think we played as well as what we have been but I still think that some of the decisions went against us," Lambert told Sky Sports.
"I didn't think it was a penalty for Fulham - I just saw it on the monitor - I saw Gabby's as well and I thought that was a penalty. I definitely don't think Fulham's was.
"I think the referee's performance for the whole game was poor. I think some of his decisions were poor."
Furthermore, an apparent elbow from Berbatov on Villa midfielder Chris Herd went unpunished, leaving Lambert increasingly bemused by the standard of refereeing.
"You look at Berbatov, he's a really good player with a lot of experience, but he wasn't looking at the ball and we got caught with that," he said.
"But as I say, I thought Mike's performance today was poor.
"Berbatov is a good player, there's no doubting that, but when you're jumping within the rules of the game, he's not really looking at the ball and Herdy's coming over him so if that's not a foul, I don't know what is.
"As I said, I thought the referee's performance today was poor. There's no point in going on about it."
Speaking of the penalty decision which allowed Fulham to double their lead, Lambert was again critical of Dean's decision making.
"The game's in the balance and the lad's played for that," he said.
"The referee's view - there's nobody blocking him - he can see it clearly, the lad's backed into him and he's threw himself. That's exactly what's happened and the referee's bought it.
"I don't think we got going if the truth be known. I can't fault the lads, their effort was there, we had a really tough game on Wednesday and you pick yourself up and go again.
"We had really good chances to get it back. If you're given a penalty, which I thought we should have been, then it might have turned.
"I think as a team, we were short. We never really got going. There's no complaints about losing the game, that's football and it happens but we have some grievances with the decisions."