The Hatters twice led on the night but the League Two side responded on both occasions, and then came up with the decisive goal courtesy of James Waite with less than 15 minutes remaining.
The Welshman, who rotated his entire starting 11, admitted: “Fundamentally you have to defend better. We are a very good side out of possession, one of the best in the Championship, but we didn’t show that tonight.
“We made eleven changes but if they want to play for Luton then you have to be good out of possession. I thought a few fell short tonight in certain moments. I thought we controlled the game in the first 45 minutes. It’s a clear foul for their goal, absolutely clear, but that shouldn’t have changed the direction of the game."
Turning his focus to the positives on the night, Jones said: “There were some moments of real quality in terms of our play and our set up. Carlos scored a wonderful goal, the second goal is a wonderful goal and you would have seen one of the best counter-attacking goals you’ve ever seen if Elliot Thorpe squared it, so there was lots of good play, it’s just we lost the game.
“I thought Henri Lansbury was excellent, I thought Tom Lockyer and Reece Burke were excellent. Cameron Jerome contributed first half, when the front two came on I thought they were really lively, I thought Elliot Thorpe looked really good and then there was a few playing out of position.
“It was a little bit makeshift but food for thought, a good run-out just disappointed because we don’t like losing games.”