Craig Morgan was dismissed 28 minutes into the 3-0 defeat at London Road and his central defensive partner Ryan Bennett also saw red in first-half added time.
"I'm loath to condemn either the referee or my players involved after only seeing the incidents once in the heat of the moment," Cooper said after the game.
"If the first challenge was two-footed he certainly deserved to go but my initial reaction to the second was that Ryan got the ball.
"Those dismissals changed a game in which we were playing really well and creating the best chances.
"Even when down to nine men our effort and commitment was absolutely first class.
"There is no getting away from the fact that the referee had a bad day on the whole. Unluckily for us, he chose to have it here."