Nyomi Fee, 28, said she found it “upsetting” to see the boy “harm” himself and not know what could be done to stop it.
Fee is on trial for a sixth week at the High Court in Livingston alongside her civil partner Rachel Trelfa, or Fee, who is 31.
Both Fee and Trelfa – Liam’s mother – deny murdering the toddler, who died at a house in Fife on 22 March, 2014, and falsely blaming his death on another boy.
The pair, originally from Ryton, Tyne and Wear, also pleaded not guilty to a string of allegations of wilfully ill-treating and neglecting two young boys over a period of more than two years.
Fee is the first witness to give evidence for the defence after the Crown closed the prosecution case on Friday.
During questioning by her defence QC Mark Stewart on the 25th day of the trial, she covered various topics including the development of Liam.
He was born in August 2011. The court heard how, by July 2012, Liam went to a childminder and his behaviour was “fine” at that stage.
But later on that year, Fee said the couple began to have concerns about behaviour in a boy they looked after, who was acting in a sexualised way towards Liam. As that progressed, she said she began to notice changes in Liam’s behaviour, including that he would pinch and bite himself.
Fee told how she voiced her concerns about the toddler’s behaviour to staff at the nursery which Liam had gone on to attend.
“Did you know as a matter of fact that there was something wrong with Liam?” asked Mr Stewart.
“No, I just had concerns,” said Fee. “He had changed. It was like he wasn’t the same little boy.
“Liam would freak out if it wasn’t me that went into the room first. He wouldn’t accept anyone coming in. He would bite his fingers, scratch himself, just get very distressed.”
Fee said she had started to raise concerns with various professionals about Liam’s behaviour around January or February 2013 and would raise the possibility that the child had autism.
“It was very upsetting to see Liam self-harming and not know why it is and what we could do to stop it,” she said.
By the time Liam left nursery in June 2013, his behaviour had continued to deteriorate, the court heard.
“It was getting progressively worse,” Fee told the court.
The trial continues.