Steve Spooner’s Blues side had a host of chances to get off the mark in the first 20 minutes, but failed to convert them and were ultimately punished.
The visitors took the lead mid-way through the first half, before doubling their advantage just before the break.
Academy coach Spooner admitted his side were victims of their own downfall by failing to take advantage when they were on top and then conceding avoidable goals.
“We started off really well and could have been 3-0 up inside the first 20 minutes,” said Spooner. “But then the game took on a whole different shape when Crewe opened the scoring and then scoring a second just before half time.
“They were both goals that could have been avoided and were very much of our own making. They came from a lack of concentration and people making the wrong decisions.
“When you’re on top like we were in the opening stages you have to score because you don’t often get sustained periods of the game when you dominate.
“In the second half it drifted away from us and I can’t really remember their goalkeeper having to make a save. We weren’t attack minded enough in the second half in terms of when we got into good positions we turned back to take a safer option.”
Blues Under-18s: Callum Preston, Josh Cogley, Dominic Bernard, Kwadwo Asamoah, Jean Kalenda (Kyle Rowley, 53), James Fry, Kyle McFarlane (Fisayo Adarabioyo, 62), Liam Truslove (Viv Solomon, 62), Reece Hales, Foday Nabay, Deqwon Ebanks.
Subs not used; Jake Weaver, Bobby Moseley.