Steve Evans was left fuming after referee David Webb admitted he got the decision to award Stoke City a penalty wrong during the FA Cup tie.
The man in the middle blew for a foul by Jonathan Tomkinson on Jacob Brown with 10 minutes remaining and Lewis Baker's smart conversion made it 3-1 and finished the fourth-round match as a contest.
But as Boro kicked off, the ref caught sight of the replay and told the Stevenage players that he had erred.
And that, coupled with a decision not given just moments before, left Evans furious.
The boss said: "We didn’t get a penalty for a handball and the referee’s excuse is that the hand is by his side.
"I’ve seen a rerun of it and his arm is out - it’s a penalty.
"And then he gives Stoke City a penalty and that’s never a penalty; it’s a great challenge.
"He then watches the replay as we kick off again and he’s told my players that he got it wrong.
"How does that motivate my players to come back in a cup tie? Somebody needs to explain that.
"He gets it wrong and referees do get things wrong, I get things wrong and we all get things wrong, players do.
"But you don’t go about rubbing people’s faces in it when there’s still 15 minutes to go in a cup tie
"You saw the added time and I would have loved to have seen that with the score at 2-1, they would have been a little bit nervous. We were testing them.
"The referee effectively kills the cup tie but we made mistakes that cost us as well.
"We’ll take the disappointment and we’re very proud of our efforts in the FA Cup but my players are really hurting."
Boro had got off to an awful start, a completely unmarked Brown firing home from a corner but after making all five changes before the hour mark, Boro levelled through Jamie Reid with 20 minutes to go.
Crucially though Josh Laurent fired Stoke back in front just three minutes before and Evans was not impressed with the defending.
He said: "It’s difficult to come to Stoke City at any time but to go 1-0 down inside three minutes is disappointing.
"It is not what we are about. There were two mistakes. We lost the header and then lost the runner and then it is an uphill task.
"We didn’t want to concede a second but when we got to half-time, we changed the shape, we changed the system and we said we had to go and believe.
"And we did, there was nothing in the second half.
"We got the goal and were comfortable but then we gave a sloppy ball away on the edge of our box."
He also addressed the reason for some of the substitutions.
"Jordan Roberts was ill in the warm-up," he admitted. "We said we’d try and start him but it became apparent after two minutes he wasn’t quite right.
"Terence [Vancooten] just felt a tightness in his hamstring. He’s pretty sore."
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