The visitors scored within the opening 70 seconds as Paris Cowan-Hall fired home from the edge of the box after Marek Stech saved Nathan Tyson's shot. They then doubled their lead six minutes before the break as Tyson converted from close range, before Elliot Lee tucked away in the 43rd minute to halve the deficit.
Tyson got his second of the evening and his side's third as he finished off a smart counter-attack after 70 minutes, before Lee hammered home after seeing an initial acrobatic effort saved with 12 minutes to go.
The result sees the Hatters remain top of the table, but the Chairboys moved into second to bring the chasing pack a point closer to the Town.
Jones said: "It was a disappointing evening. It was a wonderful game for the neutral, in terms of end-to-end chances. But it's disappointing from our point of view.
"We didn't give ourselves a real chance after we conceded after the first minute from schoolboy defending, poor defending in fact. That put us on the back foot and then to concede from a set-play, we lost two headers in the box, two things we have massively earmarked from them. So that was disappointing.
"Then we give ourselves a chance with a goal, and then we felt on the whole we were the better side. Just when we're in the ascendancy, they go on the counter attack. We have the opportunity to put two balls in their box of real quality, both full-backs hit the first man and then they break and score. It's poor really in terms of that.
"Elliot Lee then scores again and then they see the game out. When you concede three at home, it's very unlikely you win the game."