Dr. Joanne Nelson also said that abusers can "camouflage" their activities by inflicting a wound on top of an existing injury.
She was giving evidence as an expert witness at the Dungannon Crown Court trial of Millie's 27-year-old mother, Rachael Martin, and Martin's 33-year-old former lover, Barry "Budgie" McCarney.
Martin, from Main Street, Kesh, denies failing to protect Millie from the unlawful act that caused her death, and wilfully neglecting her in a manner likely to cause her unnecessary suffering.
McCarney, from Woodview Crescent, Trillick, who denies murdering Millie, is also accused of sexually penetrating the infant girl, and with unlawfully and maliciously causing the child grievous bodily harm, and causing her death by an unlawful act.
Martin's defence QC John McCrudden asked Dr. Nelson about a bruise to Millie's right ear.
Dr. Nelson said that if a toddler stumbles and falls against a hard surface it is "entirely possible for a child to sustain an injury of that nature".
She agreed that the injury could have been caused my Millie falling against a chair, adding: "I'm surprised at the extent of the bruising".
Mr. McCrudden asked her if that injury alone could have caused the "large-scale, obvious and widely distributed" bruise observed by witnesses and if someone smacking or hitting the child in that area would "camouflage" the injury.
Dr. Nelson replied: "A second injury, if it was inflicted over the first, could be camouflaged by the first."
She said she had seen this camouflage activity before and, referring to "sadistic abusers" said: "I have seen them target areas that aren't apparent, such as the soles of the feet or under the clothes".
She told the court that was why, when training doctors how to spot abuse, she tells them to take off the child's clothes and examine them "from top to toe".
Earlier the court heard that Millie took her first steps on her first birthday in September 2009, coinciding with McCarney moving in with her mother.
Mr. McCrudden asked Dr. Nelson how prone toddlers were to injury.
Dr. Nelson told the court that toddlers learning to walk "fall and stumble frequently" and "it's very common for toddlers to have bruises".
She explained that a baby's head is relatively big and the head is the heaviest organ in the body so if a child falls or stumbles "it's likely your head will hit something first" and bruising to be found around the forehead and scalp.
The doctor referred to a video, previously shown to the court, of Millie "dancing.....you can see her gait is very slightly wobbly".
Mr. McCrudden asked about the bruise-like mark found on Millie one morning, where it was indicated she might have hit her head on her cot or the wall.
Dr. Nelson said that if the child had been knocked unconscious or was vomiting or had a seizure "these would be markers of deep concern".
The doctor was asked about a second injury, a week or so later, when McCarney called Martin into Millie's bedroom and the child had a "blue lips" and bruising to the forehead.
Dr. Nelson said the lips turning blue can indicate a reduction in oxygen in the blood, where the child has stopped breathing spontaneously or been smothered by bed clothing or a hand been put over their face.
Mr. McCrudden suggested that smothering by clothing or a hand would also "suppress any noise from the child".
"Yes," replied Dr. Nelson.
Turning to the 21 rib fractures suffered by Millie, the doctor told the court "it's very difficult to diagnose rib fractures in children" adding that "it's very rare for a carer who hadn't actually inflicted the injuries themselves to realise a child has rib fractures".
She said rib fractures are "relatively common" in abuse cases and "may not, or likely not be detected clinically".
She added that it was also difficult for a "lay person, or a medical person" to detect the internal injuries of the type suffered by Millie.
Martin's defence case was formally closed today. The lawyers are now preparing their closing speeches.
The case continues.