Lord Justice Thorpe said 'procedural ineptitude' on the part of the local authority involved left him no choice but to order a re-hearing of the case.
It was meant to have been put in as evidence a week before and, although Judge Humphrey Lloyd - who heard the case at Brighton County Court - ruled it could not be used, he referred to it in his judgement.
Judge Lloyd decided that 'on the balance of probabilities' it was the mother who was responsible for harming her children.
The report, said Lord Justice Thorpe, showed 'quite a catalogue of difficulties', but because the mother's legal team did not have the time to address it, she was prejudiced by it.
Earlier Lucy Theis, for the mother, had told the judges that the report had the effect of a 'landmine' exploding underneath her case.
She argued it was akin to 'entrapment' and the mother's right to a fair hearing - enshrined in the Human Rights Act - had been violated.
And Lord Justice Thorpe said: 'It is manifest that the judgement indicates the troubled history and background as being highly pertinent.'
He told the court the mother's two young children - who are now living with foster carers - were injured within hours of each other.
It fell upon Judge Lloyd to decide whether the mother or her partner inflicted the injuries, or whether there was insufficient evidence for either of them to blamed.
Observing that Judge Lloyd was working under pressure, Lord Justice Thorpe added: 'I have every sympathy with the judg e who has a very great responsibility.
'But his judgement makes it plain he did rely on this new material.'
MEMO: THE COURT ORDERED THAT THE NAME OF THE MOTHER, FATHER OR CHILDREN MUST NOT BE REPORTED. NOTHING CAN BE PUBLISHED THAT MIGHT TEND TO IDENTIFY THE CHILDREN. ENDS MEMO
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