Steve Spooner’s young Blues side looked to be well on their way to a victory before they were pegged back.
Sam Deadfield (pictured) opened the scoring for the hosts at Wast Hills with a terrific free-kick before he scored a second with a low shot which nestled in the bottom corner.
But Crewe rallied after the break and struck twice in a matter of minutes before sealing the victory with a third goal in the dying stages of the match.
Academy coach Spooner admitted he was disappointed with the way his side capitulated.
“We were two up at half-time and well in control of the game,” he said.
“At half-time I stressed the need to concentrate because I knew that Crewe were going to come straight at us. But we didn’t and we made a mess of the kick off and they scored and then they scored again within a few minutes.
“As much as we put in a good attacking display in the first-half, in the second-half we were poor defensively. We were sloppy, didn’t pick up their players and there was distance between our players. We didn’t pay enough attention to what was happening off the ball and with our positioning and Crewe scored a winner about three minutes from the end.
“Compared to the previous week when the players looked absolutely solid as units as a back four we looked very disorganised and we threw away a good opportunity to win the game.”
Individually Spooner felt that goalkeeper Connel Trueman and goalscorer Sam Deadfield were worthy of praise, adding: “Connel Trueman in goal was excellent and showed a real level of concentration when the others didn’t and he kept us in it a couple of times in the first-half.
“With Sam we’re very pleased with how he’s developing. Technically he is very good and has that potential and if anything he needs to add even more goals to his game now.”