Mr Probert appeared to have ruled that Joleon Lescott had handled in the area, but the official later said that he had penalised skipper Kolo Toure for a foul on striker Jan Vennegoor of Hesselink.
Jimmy Bullard converted the spot kick to cancel out Shaun Wright-Phillips' strike on half time, but Hughes said: "You hope referees get the big decisions right. Unfortunately, he didn't.
"My first thought was that it was for handball but I've seen it since and it's certainly not. Now the referee is saying it's for the challenge in the box, and I'd debate that as well. It's a harsh decision. It was a coming together, not a foul.
"It wasn't a valid decision. It is obviously a key one. I looked at the video and his body language suggested he was possibly trying to indicate that it was a handball. We hear now it was a foul.
The players are down, they can see the injustice. We're not seeing games out, but today the referee played a hand. The penalty hurt us - without it, I don't think Hull would have given us too many problems
"We need to break the cycle. I sensed a bit of anxiety towards the end, which is understandable. Hull worked exceptionally hard and made it difficult, but I thought we did enough to win.
"At times we will look what we are, a team that's come together quickly and has frailties as a consequence. We are picking up points and it's only a matter of time before we're winning again."
Robinho's return was uplifting enough to earn him an ovation when he was substituted. Hughes said: "I thought we'd be delighted to get 60 minutes out of him, we got 75. He looked really sharp until he faded towards the end. He needs game time, but we're pleased he's back."
Gareth Barry was rested as Hughes paired Stephen Ireland with Nigel de Jong. Hughes explained: "We're trying to protect Gareth. He's carrying a bit of discomfort in the groin area and we want him available for the rest of the season.
"We don't want him compromised so that he can only play at 60 or 70 per cent, and we don't want his injury to become chronic. He'll be available for the Carling Cup against Arsenal."