But an investigation didn't lead to criminal charges.
Matthew Black, 19, was arrested last month on suspicion of sexually assaulting his 12-year-old stepsister.
It is the second time that Black is facing criminal charges for sexually assaulting the girl.
He waived his preliminary hearing in magistrate court on Thursday and the charges will be heard in district court. Black is charged with five counts of criminal sexual penetration against a minor under 13 years old.
Black was first arrested in September 2010 and charged as a juvenile with two counts of criminal sexual penetration against the girl. He pleaded guilty to lesser charges of aggravated battery and aggravated stalking.
He was sentenced to two years of probation, community service and counseling, according to court documents.
At his sentencing hearing in May 2011, District Judge Sandra Price told Black he was to have no contact whatsoever with his stepsister, according to a transcript of the hearing.
Initially while on probation, Black lived a distance from the victim. But, at some point, he moved in with a relative who lived close to the home of Black's stepsister and her parents, which is near Aztec, said Henry Velare, a spokesman for the New Mexico Children Youth and Families Department.
San Juan County Sheriff's Office Detective Ken Weisheit previously said Black wasn't living in the same home as his stepsister, but was living in a trailer close by.
"It's not clear if he was formerly staying there or if he was going over from time to time," San Juan County Deputy District Attorney Casey Stone said Thursday.
Velare said Black's probation officer, Andrew Caldwell, heard Black had contact with his stepsister and investigated it late last year.
"The investigation was done by interviewing (Black), as well as the family, and, at that time, nothing was found to have been happening," Velare said of the probation officer's investigation. "Whatever they found within those interviews didn't prompt (Juvenile Probation) to move any further."
The Juvenile Probation office in Farmington purged Black's file after he completed his probation, so exact dates of Caldwell's investigation were not available. But Velare said the probation officer's investigation was about a month before Black completed probation.
Black successfully completed his probation on Nov. 26, 2012, according to court documents.
The San Juan County Sheriff's Office is alleging Black started having sex with his stepsister in early October 2012, according to the documents. The alleged abuse continued into January.
"If they would have found that he was doing this while it was under our care it would have been handled differently," Velare said.
The girl's mother told deputies in January that Black was having sex with his stepsister.
The girl told detectives she had sex with Black, and investigators found incriminating messages between Black and his family, according to court documents.
Black did not admit to having sex with the girl in his messages, but he did send a text message stating that he had made a mistake and wouldn't talk to the girl anymore, according to the documents.
A warrant was issued for Black in early March but he had already left the state. He was arrested by U.S. Marshals at the end of March in Oklahoma.
Stone said that whether or not some of the assaults took place while Black was on probation for a sexual assault against the same girl will not affect his prosecution.