No-one has ever been charged over the death of a five-month-old boy who had severe bruising and anal injuries after medical experts failed to agree on the cause of death, a court has heard.

A coronial inquest has begun into the death of Michael Smedley in Alice Springs more than four years ago.

Counsel assisting the coroner, Kelvin Currie, said the baby died on July 26, 2012 while in the care of his mother's friends, Tamara Cole and Oliver Deighton.

Mr Deighton was at home on the day Michael died and had left the boy on a change table while he gave some keys to someone who came to the house about 9:40am, the inquest was told.

When he returned to the bathroom he saw the baby had wriggled to the edge of the table and was sliding off headfirst, Mr Currie said.

He said the infant was caught before he hit the ground, but Mr Deighton said Michael began hiccupping and jolting.

Michael dead with bruising, pointers to shaken baby syndrome

The inquest heard Ms Cole returned home about an hour later, at which time Mr Deighton went to get Michael and discovered him limp and not breathing.

Paramedics were called but the child was pronounced dead at 4.05pm.

But there were concerns about the death, including that the baby had 26 bruises to his body, over both bones and soft tissues, Mr Currie said.

He said Michael's body had three major pointers to shaken baby syndrome including haemorrhages to both eyes and cerebral swelling.

Michael also had anal injuries, blood in his nappy and it was thought that seven sperm heads were identified from a swab taken, the inquest heard.

Expert opinions into death differ

But medical experts consulted by police had different opinions on the cause of death.

"The initial reports supported the hypothesis that Michael had died due to trauma likely caused by abuse from a carer, probably in the form of violent shaking," Mr Currie said.

Medical personnel initially found three major pointers to shaken baby syndrome. ( Supplied: Facebook )

A biomechanical and structural engineer offered another opinion, stating the brain injury may have happened when Michael was caught as he slipped off the change table.

In 2013, paediatric forensic physician from Adelaide Dr Terry Donald provided an extensive report based on the evidence and said he believed the baby did not necessarily die from abuse and the cause of death must remain open.

Today, Dr Donald appeared at the inquest and said he now thought the death was "non-accidental" and was caused by trauma.

No sperm found on slide

Another expert consulted by police was forensic biologist Jay Gerhard who provided a review in 2015 which was critical of pathology results that had not been able to confirm Mr Deighton's DNA was on samples taken.

She told the inquest that when she looked at a slide thought to have contained sperm there was no sperm on it two weeks later.

Ms Gerhard said she had not seen that happen before, and believed it was caused by degradation of the slide because of the way it had been prepared.

"That [the different medical findings] leaves the expert opinion in a state of confusion," Mr Currie told the inquest.

"The police were unable to sustain a criminal charge and that left the mother most aggrieved."

The inquest continues.