With just 10 minutes to go, and Luton 1-0 in front, referee Darren Deadman, whom Jones was full of praise for his handling of the game otherwise, didn’t whistle when ex-Hatter Gary McSheffrey looked to have illegally dispossessed Cook.
Conor Grant picked up the loose ball and sent sub Alfie May clear to finish through the legs of Matt Macey, as Jones said: “I thought we deserved to win the game but the referee has made one mistake all day and it was the goal because it’s a foul on Jordan Cook. It’s a foul.
“I didn’t envisage them scoring, I couldn’t see them scoring and I thought we were excellent.
“I thought our game plan worked, I thought we looked really dangerous, we had the better chances and I’m proud of my team.”
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After the foul was not given, Luton were still slow to react, with a number stopping for the whistle, as Jones continued: “They’ve said that one or two switched off but I think it has gone into Jordan, it’s a foul, then we’re on the front foot to come out and then we got caught.
“It’s difficult to take from our point of view because we could have defended it better, but it’s a foul.
“That’s the only thing I’m disappointed about. But, if I’m honest, the referee was absolutely outstanding, I thought he had a great game.
“He was calm, he was assured in everything he did, so credit to him.
“But he’s made one error that has cost us, in my opinion. But, in terms of his all-round performance, I thought he was excellent.”
Cook himself, who had put Hatters in front with a fine angled drive into the bottom corner on 53 minutes, was bemused the decision wasn't given in his favour, saying: “If you look at the changing room, everyone can see that we’re disappointed.
“I think 1-1, a lot of fans would have taken that, but we were coming into the game wanting to take all three points.
“To concede that kind of goal, especially when I thought it was a foul on myself and I’ve looked at it back and it definitely is a foul, I can’t believe he hasn’t blew up on it.
“But we take a lot of positives from it. We’ve played top of the league and to me we battered them, we deserved all three points and I'm just gutted we didn’t take them back home.”
Meanwhile, skipper Scott Cuthbert, who alongside Alan Sheehan was immense all afternoon, felt that foul or not, Town should have played to the whistle, adding: "We’re disappointed to have conceded that goal. I think it was a bit naive to be honest to stop, whether we thought it was a foul or not, we should have been switched on as the boy’s got through and scored.
“So we’re disappointed with that. I’m not sure whether it’s a foul or lot, I’ve not seen it back, but it’s one of those things.”