Pathologist Dr Marta Cohen was giving evidence into the death of Mylee Weetman, from Doncaster, South Yorkshire, at Wakefield Coroners Court.
The four-year-old died in 2013 after surgery at the children's cardiac unit at Leeds General Infirmary (LGI).
However, another pathologist, Professor Mary Shepherd, said she had found no evidence of a "surgical mishap".
Professor Shepherd told the court she had examined Mylee's heart and lungs and said there was nothing to indicate complications.
She added she could not rule out rule out an air embolism.
Mylee had been diagnosed with a congenital heart defect, Tetralogy or Fallot, after her birth in 2009.
In a statement to the inquest Mylee's mother, Siobhan Casey, said her daughter had a normal childhood until 2012 when she noticed she was becoming very tired.
The operation to repair damage to her heart took place at the LGI on March 15 2013. The family were initially told it had gone well but she had suffered an allergic reaction.
It later emerged she had brain damage and her mother was told she had suffered two strokes.
Further surgery was also carried out but her condition deteriorated and her ventilator was turned off on 21 March.
Ms Casey told the inquest no-one had been able to explain to her how or why Mylee had died.
Her death came amid concerns about death rates at the unit in Leeds. Surgery was later suspended for two weeks, but a review found the centre was safe.
The inquest continues.
A child died after heart surgery because her brain had been starved of oxygen, an inquest has heard.