The offences took place in 2011 and 2012, but only came to light after the accused, now 35 years old, was arrested for assaults against two other people.
He has since pleaded guilty to multiple counts of sexual assault as well as other charges.
"In my view, if a child presents at a hospital pregnant, there's questions. There's reason for red flags to be raised," said Karen Busby, a University of Manitoba law professor and a director of the university's Centre for Human Rights Research. "Because technically speaking, an offence has occurred."
At the time, her stepfather had sole custody of her and repeatedly sexually assaulted her.
Both times she was pregnant, she had an abortion — once at a Winnipeg hospital and once at a hospital out of province.
Court documents show the girl was instructed to tell medical staff her boyfriend was the father.
According to the Criminal Code of Canada, the age of consent for sexual activity is 16, but Busby said if both partners are younger and both agreed to it, it's unlikely criminal charges would be laid.
She added even if that was her explanation, officials should have investigated it further.
"If two kids end up having sex together, probably neither of them would be charged unless someone was an aggressor," she said. "[But] if it was your boyfriend, it's still a child in need of protection. The question is, 'Is this a child in need of protection?'"
'Raises red flags'
Carol Scurfield is a doctor with the Women's Health Clinic, one of two places in Winnipeg that provides abortions.
The girl did not access her abortion there, but Scurfield said if a girl that young did show up at the clinic in need of an abortion, she would automatically be suspicious.
"In any case, if a 12-year-old is pregnant, it raises red flags that a health-care provider should be addressing, whether or not there is a child protection issue is one of those," Scurfield said.
A spokesperson for the Winnipeg Regional Health Authority would not comment on this case, but said it would also contact authorities if it's suspected a sexual assault has been committed.
They did not, however, specify whether simply being as young as 12 years old would prompt an investigation.
The accused in this case was arrested in September 2012, after he assaulted another teenage girl and her mother.
A year later, he was charged in connection with the crimes against his stepdaughter.
He pleaded guilty and is in custody. He is scheduled to be sentenced on Aug. 28.