Swindon manager Mark Cooper blasted referee Darren Sheldrake after his side were held to a 0-0 home draw by 10-man Colchester.
U's winger Sanchez Watt was sent off 23 minutes from time for aiming a head-butt at Swindon defender Nathan Thompson.
But Cooper was fuming Thompson was also booked in the aftermath of the incident, ruling him out of the second leg of their Johnstone's Paint Trophy area final against Peterborough on Monday.
Sheldrake claimed Thompson, who now has 10 yellow cards this season, "adopted an aggressive attitude" by raising his hands in the scuffle.
But Cooper said: "Nathan Thompson getting suspended is one of the worst decisions I've seen all season.
"I've just watched it back and the referee's booked him for adopting an aggressive attitude.
"If somebody comes to head-butt you and you put your hands over your face to cover it, if that's adopting an aggressive attitude, the police cells in Swindon will be very full on Saturday night.
"It was a shocking decision.
"Nathan's gutted, he's in tears because he misses the opportunity to play in the final, which shouldn't have been taken away from him.
"He never lifted his hands, he protected his face and the lad has tried to head-butt him.
"We'll have to go back to the 4-6-0. I'm sure everyone will be delighted with that, but we have to do what we have to do."
The game nearly fell foul of the weather, but a 7pm pitch inspection deemed the surface playable.
Both sides struggled with the sodden and windy conditions, with Nathan Byrne's volley over the crossbar in the dying seconds the closest either team came to scoring.