The Blades boasted a 1-0 half-time lead over their Premier League counterparts courtesy of Chris Porter's strike on the half-hour mark.
The Cottagers capitalised on their advantage and leveled matters with 15 minutes remaining through Hugo Rodallega to earn a replay at Craven Cottage, but Clough feels that referee Andre Marriner was wrong to dismiss Doyle and jeopardise his team's hopes of an upset.
He told reporters: "I thought it was incredible cup tie. It was a remarkable effort by the players - especially with 10 men.
"I thought there was more contact when Ryan Flynn went down for the penalty than there was for the sending off. The players have come off feeling a sense of injustice."
Both teams are set to discover who they face in the fifth round of the competition later today.