Abo Eisa fired Scunthorpe into the lead during the first-half but the visitors hit back to level through Jamille Matt.
Lee Novak was then sent off for an off the ball incident, which Hurst says the club may appeal.
Moments later, Padraig Amond scored the winner to send the Exiles home with all three points.
The boss said: “It was a poor game. It was a tough day for different reasons. In the second-half they certainly put us under pressure.
“We felt we stood up to that really well in the first half, albeit in different conditions. The sending-off happened and I’m not convinced about that at all. We then conceded pretty much straight away, which made it extremely difficult for us.
“They then used ‘game management’ and that’s where you need the referee to intervene, and I don’t think he’s had his best day today. He missed a blatant red card for a tackle from Ryan Inniss on John McAtee in the first half, with a straight leg around John’s knee, and we’re very lucky that he didn’t get seriously hurt from it.
“Overall, we didn’t do enough even at the start of the second-half in terms of trying to get out and make it more difficult, retaining the ball more. They just kept pumping it back in, and we didn’t get high enough up the pitch either to try and help solve that problem.”
Talking about the Novak dismissal, he said: “We’ll have to look at it certainly. Novs does move his arm, I’m not denying that, but I don’t think there’s any real contact. He’s actually getting fouled and that’s why he turns and reacts a little, but to be a red card, I’m struggling with.”
There were four changes to the starting line-up, and the boss stated: “As I said in the press yesterday, we’ve suffered with Kevin’s injury (Kevin van Veen missed out with a dead leg), while Alex Gilliead was ill.
“Rory McArdle hasn’t overcome his illness, although he was in yesterday, did a jog and felt alright. As soon as he joined in a game, he was struggling. He was here today to cheer on the lads but he’s ill.”
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