The pair both saw red for tussling over the ball in the back of the net after Chris Mepham's debut goal for the Bees cancelled out Chris Basham's opener.
Wilder said: "I'm not really sure what he was thinking about dealing with a 6ft 7in lad. Jamal doesn't have to hand the ball back. Woods has a slap and Jamal retaliated and made it easy for the ref.
"It's frustrating for both benches because the ref missed quite a lot for both sides during the game but not that incident, and we both lose good players for three games. For me, not every tackle is a yellow card in the conditions."
Wilder paid tribute to Brentford, adding: "It was an excellent game between two different teams. I have nothing but respect for Brentford in the way they play and recruit.
"The organisation of the team was really good and we had the best chances in a tough game where both teams went for the win. We haven't gone anywhere and set up to frustrate. We came for the win, as shown by the chances we've had."
Wilder admitted his side were "disappointed and frustrated but not in a bad way" at being pegged back, but added: "Brentford have beaten better sides than us but we are in a good place going into last seven games of the season.
"Every game in the Championship is a pleasure to be involved in. We have gone toe-to-toe with a really good team and if we finish ahead of Brentford it will be a great achievement because they are excellent."