The disagreement took place last week and required intervention from the club before the matter was resolved.
Cestero had been named among the Castilla substitutes against Sant Andreu, although his omission from the starting line-up initially appeared to be linked to the workload he had accumulated in the days before.
The midfielder had played 80 minutes in the Juvenil A side's 3-1 victory over Santiago Wanderers in the Under-20 Intercontinental Cup final at the Santiago Bernabéu.
López de Lerma did not disclose the reason for Cestero's absence against Alcorcón but stressed the developmental nature of the Castilla setup and insisted that the player remains an important part of his plans.
"We are in a development environment. We want all the players to be able to show themselves, compete and be part of the team," the coach said.
"Jorge will be a very important player for us this season."
The decision nevertheless meant Cestero missed the latest match, which Castilla lost 2-1 to Alcorcón.
The midfielder had already made a strong impression during the campaign, including scoring his first goal of the season, and has established himself as an important member of the reserve side.
His progress had also been recognised during pre-season, when he worked with José Mourinho's first team. Cestero featured in all four of Real Madrid's friendly matches during the preparation period and was one of the academy players given significant opportunities.
The episode with López de Lerma has now been considered resolved inside the club, leaving Cestero's next opportunity to return to the squad potentially coming in the Madrid derby.
His development remains a central part of Castilla's season, with the midfielder having already moved between the academy and senior environment during the opening months of the campaign.
For López de Lerma, however, the message around the squad has been consistent: players are expected to compete for their places while continuing their development.
Cestero's omission against Alcorcón was the immediate consequence of the disagreement, but the coach's public comments also made clear that the midfielder remains part of his plans for the season.