Monaghan boss Malachy O'Rourke claimed referee Joe McQuillan was inconsistent in awarding the free from which Armagh earned an Ulster semi-final replay.
The Cavan official gave the stoppage-time free for a jersey pull on Armagh's Aaron Kernan, and Rory Grugan slotted over the levelling score.
It meant the teams will replay at Clones on Sunday, 6 July.
"If you are going to give them in the last minute, you have to give them during the game," said O'Rourke.
"There had been other challenges like that which went unpunished and that is why it was a wee bit harsh.
"The referee said was for a jersey pull, and maybe that was right - but it was not the only jersey that was pulled during the match.
"The referees do not have an easy job and he made the decision as he saw fit, but it was very disappointing for us.
"Fair play to Armagh, though, coming back so well and we have to do it all again."
Manager O'Rourke was also unhappy with the black card decision which resulted in skipper and star forward Conor McManus having to be replaced early in the second half.
McManus was punished for a late challenge on Finnian Moriarity.
"It looked innocuous enough to me. Maybe he did trip the fellow coming out but it wasn't dangerous and wasn't going to change the course of the game," said O'Rourke.
"It just seemed a very harsh punishment for something like that."