But after Roberts was charged with murder, and she had an independent pathologist explain to her the full autopsy report, she changed her mind.
"I now accept that James killed Leon," she told an inquest into Leon's death in Christchurch today.
"It took me some time to come to that conclusion, as I trusted him and I loved him."
Child, Youth and Family said it had worked with the family but investigations "did not establish evidence of physical abuse".
Coroner Brigitte Windley is presiding over an inquest into Leon's death.
Mother invokes legal privilege
Roberts invoked a coronial court privilege against self-incrimination during her emotional evidence today.
She refused to answer questions surrounding a hole in the plasterboard at the Lambeth Cres property.
Roberts denied that her husband had tried to explain the hole in the wall to her during phone conversations on the day Leon suffered his fatal injuries.
Counsel assisting the coroner, David Boldt, questioned how she was able to explain detail the plasterboard damage if she hadn't seen it before.
A midwife told police how Roberts, at Leon's side in ICU, had spent "most of her time" on the phone to Roberts.
"The police think he's done it. There's no way he could've done it," she allegedly told the midwife.
She was worried about coping without her husband if he was charged with murder, the inquest heard.
"How would I live without him? I need him by my side," Roberts allegedly told the midwife.
Police bugged the Roberts' house after Leon's death, the inquest heard.
During Leon's wake at the property on June 1, 2015 James Roberts was heard joking, "We should kill a kid more often", after they received a lot of gifts are the death.
Emma Roberts said she was "not happy" with the remark, and although a "very poor and tasteless attempt at humour", she did not take it as an admission of guilt by him and didn't think any more of it.
Stepfather a regular drug user
Detective Sergeant Chris Power, who was second-in-charge on Operation Lambeth, the investigation looking into Leon's death, said Roberts was a regular user of drugs, including heroin and cannabis.
He considered it "likely", given Roberts' habitual drug use, that he was affected by drug-taking when Leon was in his care the day he suffered his fatal injuries.
Text messages recovered from Roberts' phone was "absolutely littered with drug talk, drug use", Power said.
"There was extensive drug use by him," he said.
Power said Roberts talked about coming home and "lighting up" and smoking on the couch or in the kitchen.
Roberts had an "inherent predilection" towards anger, violence, and bullying, Power said, which was triggered by drug use or when angered at being challenged.
While Power accepted there was considerable potential for the autistic Leon to injure himself, he believed that the boy's fatal injury was a culmination of physical assaults by Roberts on him.
Of Leon's 44 injuries identified in the post-mortem examination, police were not able to say if all the injuries occurred on the same day.
The inquest has been adjourned part-heard. A second hearing could be held at a later date.
