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.

All of this weekend's matches in the Champions Cup and Challenge Cup due to have been played in France have been called off.
Bath Rugby tweeted: "Our thoughts are with all those affected by the tragic events in Paris, and safe travels home to everyone in France."
Toulon have won three successive European titles.

Douglas Herridge, 18, hit Colin Payne at the family home in Dartford, Kent, in November.
Jurors at Maidstone Crown Court heard Mr Payne intervened in a row over money between the teenager and his mother.
Mr Herridge said the 54-year-old grabbed his neck and tried to throttle him, when he struck the blow.
Home Office consultant pathologist Dr Richard Chapman said Mr Payne, a former national squash champion, died from a blow of moderate force that damaged a vessel carrying blood from the heart to the brain.
Judge Jeremy Carey, presiding, said: "The word tragedy is probably overused, but this case can truly be described as tragic.
"Colin Payne was on everybody's assessment a fine man, a distinguished amateur sportsman, a good father, and a responsible and decent member of society, and he came to an untimely death in circumstances that really were absolutely devastating."

King Arthur Pendragon argued a parking fee of £15 for the 2016 summer solstice breached his human rights.
At an initial court hearing in January, Mr Pendragon said the claim was not about money or costs, but because the fee "unfairly targeted his religion".
But Salisbury County Court ruled that introducing car parking charges was a "reasonable and legal measure".
Mr Pendragon had argued that this treatment was in direct violation of his human rights and that he has a right to worship at Stonehenge without unnecessary restriction or hindrance from English Heritage, which he claims is merely managing the site "on our behalf".
English Heritage said it introduced the parking charge to encourage more people to car share or travel by bus.
However, Mr Pendragon said he wanted to prove English Heritage was wrong to turn him away when he refused to "pay to pray".
A childminder has been telling the Liam Fee murder trial that she had concerns about the toddler.
[NEXT_CONCEPT]
Bath's European Champions Cup match in Toulon on Sunday has been postponed following the deadly attacks in Paris.
[NEXT_CONCEPT]
A teenager who fatally struck his stepfather with a single punch to the head has been cleared of manslaughter, because he acted in self-defence.
[NEXT_CONCEPT]
A senior druid has lost his legal challenge with English Heritage over car parking charges at Stonehenge.