Ms Martin also said Millie had begun to cry whenever she said good night.
BBC: Millie Martin trial: Mother sobs during court questioning
Ciaran Murphy QC said Millie had been the victim of serious physical abuse, a sexual assault and a significant head injury which caused her to die.
In the afternoon, the trial heard from Mairead McGinn, a consultant paediatrician at the Belfast Trust, who said Millie had been essentially brain dead when she was taken to the Royal Belfast Hospital for Sick Children.
She said Mrs Graham had recalled lifting Millie and the child had winced and said "sore, sore, sore".
Ms Martin said that when Millie had a large bump on her forehead, Mr McCarney had told her she must have hit it on the side of her cot.
She said she had asked Millie's mother when the toddler had last been well.
Earlier, Mr McCarney's barrister said she accepted that Millie's injuries had been deliberately inflicted.
She said the night before Millie was taken to hospital the toddler had been fine.
She has previously said this happened when Millie accidentally touched a candle flame.
Her mother said she had put Millie to bed leaving Mr McCarney in the house while she went to get a carry out.
Sculptor Ross Wilson said he hoped 'Millie' would "help explain the significance of the Greater Shankill area to Belfast's history to local people and visitors alike".
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.
She said that when she told Millie's mother this, she had asked her how the injuries could have happened.
But the next morning she said she was surprised when Millie was very sleepy and appeared to be coming down with the cold.
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".
When she brought Millie to her mother's house she said her daughter's condition had them in tears.
Ms Martin was taken through the injuries Millie had suffered before her death, but said that, apart from seeing her daughter hit her ear on a chair, her other bruises were "unexplained".
BBC: Millie Martin trial: Mother sobs during court questioning
The doctor also said that Ms Martin's mother Margaret Graham had said she had noticed something when changing Millie's nappy.
She said at that stage she believed that Millie had had a fit and Mr McCarney was doing everything he could to save her.
BBC: Millie Martin trial: Mother sobs during court questioning
She said that, up until the night of Millie's death, she had trusted Barry McCarney "100%".
Had she taken steps to remove Millie from Mr McCarney's presence, the prosecutor said "this child would not have died".
Ms Campbell said both women were extremely distressed that someone could have harmed Millie.
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".
She said it was only when they were told at the hospital that Millie had been "improperly interfered with" that she started putting everything together.
BBC: Millie Martin trial: Mother sobs during court questioning
The barrister said Mr McCarney told police that on the day he had rushed Millie to hospital he had finished work earlier because he had felt unwell.
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.
"Millie will always be missed and she will certainly never be forgotten, " they said.
He said Rachel Martin had done nothing to seek intervention and that the injuries Millie had "were too significant, too severe and too many" for her not to have known Millie was being abused.
"I'd never seen Millie ill before and it broke my heart for her to look like that, " she said.
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