It was an eventful afternoon for striker James Collins who gave the Town the lead just after the half hour mark, before picking up two yellow cards midway through the second half. Jabo Ibhere made an instant impact after he came on as a substitute, heading in Halliday's cross late on, before the Hatters had to weather a late Cambridge storm.
With all but two of the Sky Bet League Two fixtures going ahead after a few days of bad weather, the result moves the Hatters four points clear at the top of the fourth tier.
Jones said: "I am disappointed again, obviously. We were cruising in the game without any problem whatsoever, without being brilliant, just effective. We couldn't get the second goal and it all changed on a decision.
"For me James was silly for his first yellow, and then when you're on a yellow, don't get involved with stuff like that. The referee I felt could have handled it better, I've spoken to him already and he has thanked me for my attitude and the referee last week thanked me for the attitude and the way I speak, it doesn't do me any good.
"It's clearly a goal kick, not a corner. But Collins has gone about it the wrong way and has gone with his arms open and apparently the letter of the law is if you go to a referee with your arms open you get a booking. I felt he could have handled it a little bit better.
"It's a big game and there is a lot of enthusiasm and desire goes into these games. He made a mistake, Collo made a mistake coming up to him. That changed the game and we were backs to the wall and we had to defend out for a point. We were absolutely controlling the game and cruising."