The Alex boss admitted that his team started the evening poorly, and lamented his side's inability to build on their recent Johnstone's Paint Trophy success.
"It was a disappointing night for us. After the terrific performance that we put in Sunday we couldn't follow it up. Brentford started the game like we started the game against Southend," he told the club's website.
"We started the game poorly and I have had a go at the players for that. We gave them a foot-hold in the game and made it very difficult for ourselves. After the first 20 minutes we started to play and compete but never really created chances.
"Brentford were very competitive and powerful. We think they are the best team that we have played and we struggled to cope with that."