A day care employee found 3-year-old Myles Hill inside the van, and he was pronounced dead a short time later, police said.
Investigators said that St. Charles wasn't an approved driver on the facility's roster.
On Thursday, day care officials said the employee, who has not been named, was not authorized to drive the van.The worker was sacked after the incident, and is expected to face charges in Myles' death, the report says.
The Orange/Osceola County State Attorney's Office and Orlando Police Department could not be reached for comment.
But parents arrived to drop off their kids on Tuesday and said they had not been told of the tragedy.
St. Charles was the driver of the van for Little Miracles Academy. St. Charles assumed that everyone had gotten off but "admitted to failing to perform a head count to be sure", the affidavit notes.
UPDATE: Deborah Denise St. Charles, 51, has been arrested for Aggravated Manslaughter of a Child in the death of 3 year old Myles Hill. She handed some of the cleaning supplies to the kids and closed the van door assuming that all the children had gone inside.
During the pickup, Myles' grandmother, Brenda Watts, provided St. Charles with the payment for Myles' childcare and placed him in the back of the van on the driver's side, the affidavit states.
When St. Charles drove the van to a second Little Miracles location, she allegedly forgot to check the vehicle for children.
Myles was marked "present" by staff at Little Miracle Academy II, which is a violation of DCF attendance record keeping, the report said. When St. Charles parked the van she received a phone call, and was on the phone when she grabbed her personal belongings and locked the van without looking around, the report shows.
The medical examiner listed the cause of death as "hyperthermia due to environmental exposure" and the manner of death as an accident.
Temperatures inside the van were as high as 144 degrees at 3 p.m., investigators said. Thornton owns two facilities, and they have both been shut down pending a thorough investigation.
Orlando police Chief John Mina said Myles was supposed to have been dropped off Monday morning at another day care centre but instead he was taken to the location where his body was later found. "We will continue to aggressively act to keep kids safe and will hold anyone accountable who doesn't follow the law", a DCF spokesman said. She then walked into the day care and into her classroom until she left for the day at about 6 p.m.
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