Quickfire goals from Adam Forshaw and Marcello Trotta midway through the first half did the bulk of the damage, with Sam Saunders adding a third after the break after Joel Garner missed a penalty for the hosts.
The result extended Brentford's unbeaten sequence in League One to 10 games and means they continue to breath down the necks of the division's pace-setters.
"I am disappointed that we lost the game and conceded three goals and have not scored any," said Grayson. "They got the penalty decision and the goal straight after so I'm disappointed to go in two-nil down, there was not much in it.
"I asked for a reaction from the players - to get amongst them and win their individual battles and show more quality - and the next goal was going to be a big part of it.
"It was a great opportunity for Joel (Garner) to put the penalty away and Kevin (Davies) had a chance with the header and we had the momentum really going then. Unfortunately they got the third goal that killed the game off.
"We knew it was a tough game but too many of our players lost their individual battles all over the pitch and we did not have the right quality at times and we made wrong decisions."