Heather Farmer told the jury that in the five years she had been a registered childminder, Liam was the only child she had concerns about.
Rachel Fee, 31, and her partner Nyomi Fee, 28, deny murdering Liam in March 2014 at a house in Glenrothes, Fife and ill-treating two other boys.
Ms Farmer said she had looked after Liam since the summer of 2012.
The jury heard Ms Farmer kept a diary during the time she looked after him, noting he had bruises on a number of occasions.
She said by Christmas 2012 she had begun to have doubts and contacted the Scottish Childminding Association for advice because she thought " somebody was hurting Liam."
Rachel Fee and Nyomi Fee, who are originally from Ryton, Tyne and Wear, are accused of murdering Liam in March 2014 and attempting to defeat the ends of justice by blaming the killing on a young boy.
The couple are also charged with a catalogue of allegations that they neglected Liam and abused two other children, one of whom they blame for killing Liam, in their care over a two-year period.
They deny all the charges against them.
The trial at the High Court in Livingston continues.
A childminder has been telling the Liam Fee murder trial that she had concerns about the toddler.