A Michael Turner header 11 minutes from time sealed the points for the visitors from a game that Clive felt become slightly disjointed due to some fussy refereeing decisions.
"We are disappointed that we have lost the game," reflected Clive afterwards. "I know the lads are disappointed with the way they've played although I thought the flow of the game was interrupted by a lot of petty decisions by the referee.
"It looked like it was going to be a goalless draw and, obviously, we didn't create as many chances as we would have liked to. I thought we looked the more likely of the two teams to win it, but it is all part of the learning curve for the boys.
"It is a disappointing result and one that I hope the boys will learn a lesson from."
The young second string looked as though they were imposing themselves more on the game as the second half progressed, but were left deflated when passages of play such as a delightful Jonathan Blondel spin to lose his marker and run on goal was, for some reason, decreed illegal.
"That was the frustrating thing about it," added Clive. "We couldn't get many constructive moves going as there were too many breaks in play. He certainly wasn't looking to play the advantage and it almost became a non-contact game - and I've never known football to be that.
"From that point of view it was a shame, but we weren't bright enough in the final third and delivery was poor. We didn't create enough chances and it is something we're going to work on."
Clive Allen admitted that he was disappointed with the display of his reserve team charges following the narrow defeat to Charlton Athletic at Stevenage on Monday evening.