The accusation claims the boys crawled through a hole in a fence during playtime just outside the facility along 100 S. Atchison St. on August 20. It says a lone teacher was supervising 13 preschool-aged children at the time, one more than the 12 child maximum set by Social Services.
The two boys were discovered missing during a head count at least 30 minutes later.
Witnesses spotted the boys on nearby Metrolink tracks and called Anaheim police.
They were unharmed, but Metrolink runs trains through that area about every half-hour on weekday afternoons.
The department also accused the Children's Station of failing to inform police and parents when it was realized the children were missing, as required by Social Services, and failing to establish written procedures for signing children in and out of the facility.
The mother of one of the boys that went missing, Vanessa Hughes, disagrees with the move to revoke the facility's license, saying she'd rather see the incident serve as a lesson for day-care facilities to create more structured procedures.
"You hear about earthquake drills, and those don't happen very often; how odd is it that in a child-care facility there isn't a drill in place for a missing child?" Hughes said.
"We've been proactive in enhancing our child-safety policies and are working with Community Care Licensing, our stakeholders, our staff and our families to ensure the highest level of quality at our center," Paul Andresen, president and CEO of Anaheim Family YMCA, said in a statement Monday.
The day-care has 15 days to appeal, in which case, it will be presented to an administrative-law judge.