The Giallorossi were unable to find a way back into the game after Felice Cimino opened the scoring on the stroke of half time. Andrea Tripicchio then doubled the hosts' lead when he converted from 12 yards in the 77th minute.
Following last weekend's reverse at home to Pescara, the U19s' second consecutive league loss means they slip down to third place in the standings, with Empoli and Frosinone moving above them.
After the game, Alberto De Rossi said his team were suffering from mental tiredness.
"Like all teams we have our problems and they tend to surface when we're lacking a bit of mental energy," he explained. "We struggle to play our normal game when there are lots of matches close together. You might say it's physical fatigue but I don't think it is that. I think we find it hard to maintain the right level of concentration for these matches. We conceded from a set piece again, leaving one of their players completely unmarked, and that's a sign that we're not fully switched on."
The Giallorossi coach did admit that the hosts were good value for the three points.
"Crotone played really well. They looked bright and determined for the whole 90 minutes and seemed to know what they wanted to do with the ball. They were deserved winners."
With Frosinone and Empoli both winning elsewhere, Roma now find themselves pushed down to third place.
"It's a shame about our league position but I actually think it will do us good," De Rossi continued. "It will give us something to think about and make us realise that, yes, we are a good team but we need to play at 100%.
"Another thing we should remember is that besides doing well in the league our job is also to prepare players for the first team and we have two guys with lads at the moment. That's important too."
Ahead of next week's visit of Lazio to Trigoria, the Primavera boss wants to see a return to old habits.
"Regardless of the motivation a derby always brings, we must get back to dominating games again, bossing possession and harrying our opponents all over the pitch."
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