The Spanish champions are currently enduring an injury crisis at left-back, but the Portuguese coach has opted to use midfielder Michael Essien as a makeshift defender rather than Nacho, who came through the ranks at the Bernebeu.
"We play with a different system, they have another model," he told reporters.
"There are Castilla players that play in positions that do not exist in the first team, like Jese [Rodriguez] who plays as a 'nine and a half'.
"Also, our wide players play further forward, and in Castilla they play a 4-4-2. There is limited common ground in terms of the style of play, and the kids are the ones who end up paying the price."
Mourinho has however, called up three youngsters, Jose Rodriguez, Alex and Ruben Yanez to the squad to face Alcoyano in Copa Del Rey on Wendesday, with the likes of Cristiano Ronaldo and Mesut Ozil rested.