The Scottish consultant reported that Millie's rib injuries were non-accidental and that, since it was difficult to injure the ribs of a 15-month-old infant, they must have been caused in Millie's case by "severe gripping or squeezing".
Earlier, Mr McCarney's barrister said she accepted that Millie's injuries had been deliberately inflicted.
The doctor also said that Ms Martin's mother Margaret Graham had said she had noticed something when changing Millie's nappy.
She said she had asked Millie's mother when the toddler had last been well.
She said that, up until the night of Millie's death, she had trusted Barry McCarney "100%".
She was asked about a bruise seen on Millie's head in a number of the photos.
Millie's mother, Rachael Martin, was cleared of allowing her daughter's death, and cruelty through wilful neglect.
An inquest into Millie's death was opened and adjourned until April while investigations are carried out.
Instead, they have established Millie's Trust charity to pay for parents to have first aid lessons.
She said that when she told Millie's mother this, she had asked her how the injuries could have happened.
Ms Martin also described how Millie's behaviour changed leading up to her death.
BBC: Millie Martin trial: Mother sobs during court questioning
Barry McCarney, 33, from Trillick, sat in the dock alongside his former partner Millie's mother, Rachel Martin, 27, from Kesh.
She was also asked about a burn which can been seen on Millie's finger in photos taken just days before her death.
Another doctor told the court she was so worried by the range and nature of Millie's injuries she contacted the police and social services.
However, in baby Millie's case there was no need to put her asleep, and that her pupils were fixed and did not respond to light.
Capitale Douala, three doors down from Millie's, cooks up African specialties.
He carried out a post-mortem examination of seven of Millie's ribs which he said showed no evidence of disease, adding that fractures to them were about four weeks old.
After the verdict was delivered in Dungannon Crown Court, Millie's mother, Rachael, sobbed uncontrollably in the dock and cried "thank you, thank you, justice has been done for my daughter".
Mr Murphy said that one medical expert who had examined the fractures to Millie's ribs, claimed the force required to cause such injuries was akin to something "like a road traffic accident".
The prosecution alleges Mr McCarney was responsible for causing Millie's injuries and that his ex-partner Ms Martin "wilfully closed her eyes to what she knew or ought to have known was happening".
The court had heard that McCarney began a relationship with Millie's mother at the end of August 2009 and moved into the family home between the end of September and start of October 2009.
Earlier, Dr Rheem Mabrouk, who was the first doctor to see the toddler on the night she died, told the court she was so worried by Millie's injuries when she was admitted to hospital, that she immediately contacted police and social services.
When she brought Millie to her mother's house she said her daughter's condition had them in tears.
Had she taken steps to remove Millie from Mr McCarney's presence, the prosecutor said "this child would not have died".
At one stage he gave the child mouth to mouth resuscitation, and pumped her chest a few times, before rushing to a neighbour's house with Millie in his arms.
On the opening day of the murder trial at Dungannon Crown Court, prosecution lawyer Ciaran Murphy QC said that Mr McCarney was initially arrested on suspicion of sexually abusing Millie, but following the toddler's death, the defendant was questioned by PSNI detectives over a three-day period.
The family, including Alex's brother Ben, 16, and sister Millie, 14, is looking forward to a holiday to Florida in October, courtesy of the Make a Wish Foundation.
Later, Tony McHugh, Mr McCarney's former boss, said that on the day Millie was rushed to hospital, he had turned up for work as normal on the site of the new Erne Hospital, and that "he seemed fine".
Josephine McCaffrey said when she arrived at Mrs Graham's home, Ms Martin was in the house with Millie.
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