Daniel Powell struck twice, with Paul Green also scoring as the home side emerged victorious at the Alexandra Stadium.
Lee Novak pulled a goal back for the Iron with ten minutes left and the score at 2-0, but Scunthorpe conceded soon after as the hosts sealed the win.
Speaking afterwards, Hurst said: "We weren't at our best but at the same time I think we have to acknowledge we came up against a very good team. They haven't won every single game they've played, but I've seen some really good performances from them. Today, if you came as a neutral, you'd have gone away thinking they were an excellent side.
"Obviously you have to try and stop that, but they played some really good football and I'm struggling to think of a better team I've seen in League Two in all honesty, but that's what we're wanting to strive to be, and today we were certainly second best.
"I don't think we quite had the energy, or the quality enough times. I thought we had some spells where we kept the ball and passed it, but we didn't find our spare man anywhere near as well as what Crewe did. I felt there were times where Kev (van Veen) found positions in the first half but we didn't seem to find him, whereas Crewe always did find their man.
"Our goal came from a good finish from Novs, who worked tirelessly today I felt, and then we pinched the ball off them quickly after and almost got in a position, and we could have made it a nervy last 10-15 minutes. To concede two minutes after the goal though took the wind out of our sales.
"Crewe are a very young, energetic team and they showed today that if you take care of that football you can make it very difficult for the opposition."
van Veen came off at half-time, and Hurst said: "Kev was feeling ill going into the game. We got 45 minutes out of him but I don't think he was quite right so I probably made a mistake there in terms of playing him. He was struggling earlier in the week and trained well yesterday, and we thought he was over the worst of it. Today in the hotel I had a chat with him, and he felt he could certainly give it a go, but he wasn't quite right in how he felt and his ability to make forward runs, etc wasn't there. We asked him just prior to half-time to wait until half-time so we could make it clear to the group how we were going to set-up."
Hurst also explained a knock for James Perch, adding: "It's something he's felt in the last couple of games, so we'll see whether he's going to be okay or not. He's a tough lad and wants to play, and didn't show it in his performance as he was still running right until the end, but we'll have to see how that settles."
There was just one change ahead of the game, as Matthew Lund came in for Jacob Bedeau, with Hurst explaining: "I think Lundy realistically would have played the other day (against Walsall) had he been fit enough at that stage. He did some running prior to the game and felt very tired, but has felt better since.
"Jacob is a bit unlucky because he did well the other day, but we wanted to get Lundy back in, and revert to four at the back."
Meanwhile, he also touched on the absence of attacker Jamie Ward from the substitutes bench, explaining: "That's just tactical. I spoke to Jamie and explained my reasoning. We wanted another out and out forward on the bench and I felt it might be a game George (Miller) could be suited to."
When asked whether Jake Eastwood, missing for the second game in succession with a groin injury, would be back available for selection for the away game at Oldham Athletic on New Year's Day, the boss continued: "I hope so. He's making progress, and it wasn't a really bad injury. Hopefully he'll be back for the next game."
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