The first indication of trouble came in the form of Rilya Wilson’s case file: It seemed unusually thin.

State child welfare worker Dora Betancourt, who took over the 5-year-old foster child case in April 2002, examined the paperwork and noticed that no one had checked on Rilya in more than a year.

After a series of phone messages to Rilya’s foster mother, Betancourt came face-to-face with Geralyn Graham in the driveway of her Kendall home.

“Where’s Rilya?” Betancourt asked.

“Oh, I thought you were bringing her back,” Graham said, according to Betancourt, who testified Wednesday during Graham’s murder trial in Rilya’s disappearance.

Betancourt told jurors Wednesday that Graham’s story unfolded in a bizarre and confusing fashion. She said an unnamed Department of Children and Families worker whisked the 5-year-old away for some sort of mental health evaluation more than a year before.

“I was in disbelief,” Betancourt told jurors. “I asked her, ‘You mean, you haven’t seen her in over a year and a half?’ She said, ‘No, I don’t know where’s she’s at.”

“Did you find that her explanation made any sense?” Miami-Dade prosecutor Sally Weintraub asked.

“It didn’t make sense at all,” Betancourt replied.

Graham, 66, is charged with first-degree murder, aggravated child abuse and kidnapping in the slaying of Rilya, whose body has never been found.

Miami-Dade police eventually took over the investigation. In 2005, a grand jury indicted Graham after she allegedly confessed to a jail cellmate that she smothered the child and disposed of her body in a South Miami-Dade waterway.

Prosecutors are also relying on Graham’s conflicting statements about what happened to the girl.

DCF had placed Rilya in the custody of Graham’s live-in lover, Pamela Graham, no relation, although jurors heard that Geralyn ran the household. Geralyn repeatedly told welfare workers that the two were sisters, a fact prosecutors say is not true.

The Rilya case caused massive upheaval and reform at DCF, which did not notice the girl was missing until April 2002, more than one year after Rilya was last seen alive.

Betancourt, then a case worker in the agency’s adoption unit, testified that her unit received the case in April 2002. That conflicts with the testimony of Rilya’s original caseworker, Deborah Muskelly, who told jurors Tuesday that she stopped working on the case in January 2001 when the case was transferred to the adoption unit.

Muskelly admitted she filed false travel reports for phantom visits to Rilya’s home, and substituted phone calls to Graham for physical visits to the house. Muskelly was arrested and served five years probation for falsifying DCF time sheets.

When Betancourt finally made a home visit, Graham told the case worker that Rilya began exhibiting strange behavior in 2001, urinating and defecating on herself during nighttime walks. So Graham claimed she left messages at DCF’s child protective unit.

Graham claimed that a DCF employee, presumably responding to the messages, picked up the girl. Another employee came weeks later to pick up Rilya’s toys but offered no information on the child’s whereabouts, she claimed.

Betancourt found it odd that Graham – who claimed to be the girl’s paternal grandmother – never seemed upset that the child had been missing for so long with no explanation from DCF, and that she never followed up with the agency to find out where Rilya was.

Betancourt immediately notified her supervisors, two of whom testified Wednesday that no DCF or court documents existed showing Rilya had been removed from the home. A judge must approve the removal of any child from a home, generating a flood of paperwork, they said.

In the scramble to figure out what happened, Betancourt and supervisors discovered that Graham had been receiving financial assistance from DCF for Rilya throughout the months the girl had been gone from the house.

To get the benefits, prosecutors say, Graham turned in a sham court order naming her as a “relative custodian,” even though she was not.