Dr Babani said that he checked Brandon's body shortly after his death and found "multiple bruising" with some around the abdomen, right leg and back.
He said: "We had a doubt about the nature of the bruising."
The doctor told advocate depute James Wolffe QC, prosecuting, that "typical" bruising for a child would be on the hands, fingers and shins.
Brandon Muir died after his intestine ruptured
He later met with the dead boy's mother at Ninewells hospital to discuss the death.
Dr Babani said: "We asked the mum about the bruising and she did not have any explanation for this."
The court had earlier heard from a nurse who said she had given Brandon Muir an immunisation jab at Dundee's Lochee Health Centre, three days before he died.
Nurse Donna McKeever said there had been a general failure to bring the child to the clinic to be immunised.
She also told the trial that Ms Boyd had no concerns about her son and that he had been "well".
The nurse said Boyd also met social workers while at the health centre that day.
Dr Babani was the final prosecution witness in the case. Jurors are due to find out on Wednesday how the defence case will proceed.
Mr Cunningham is accused of murder by assaulting Brandon so severely on 15 March last year at two flats in Balunie Crescent that he died the following day in hospital.
Mr Cunningham and Ms Boyd, 23, also face a charge of repeatedly and wilfully ill-treating Brandon between October 2007 and March 2008.
Ms Boyd is accused of assaulting her son at Douglas Family Centre in Dundee on 5 March last year.
Mr Cunningham is also charged with repeatedly and wilfully ill-treating another young boy at properties in Dundee between October 2007 and March 2008.
The pair deny all charges.
The trial, before Judge John Morris QC, continues.
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