Stevenage boss Graham Westley felt hard done by after seeing Rotherham's first goal awarded in his side's 2-1 defeat.
Video replays showed Wes Thomas' opener for the Millers was onside despite what appeared to be claims from Stevenage to the contrary.
But Westley stressed afterwards that his players were not claiming offside but felt there was a foul on goalkeeper Chris Day.
Francois Zoko duly slammed home an 86th-minute equaliser for Boro only to see Lee Frecklington snatch an even later winner for the hosts.
"I feel for the lads, they have put a lot of work in and they have spent themselves and their shirts on the pitch," Westley said.
"We played some really good stuff and we created a lot of chances but football can be cruel sometimes and it was certainly cruel to us .
"With the first goal we were devastated we didn't get the decision. The goalkeeper has got the ball in his hands and Alex Revell made no contact with the ball. I've looked at the video and nine times out of 10 you see a free-kick in that situation.
"I find it tough to accept that there is no foul involved. The offside situation was fine, we weren't appealing for that.
"Rotherham are going well, they have got good home form and good general form and Steve (Evans) has got them going well .I thought our lads were terrific. They took the game to them, they kept their focus and sense of purpose."