A four-year-old girl and her three-year-old half-brother are to be adopted after twice being removed from their mother and her partner by Wiltshire Council social workers.
The youngsters were taken into care in 2011, returned home in March 2013, then taken back into care in June 2013.
Their mother and her partner - who is the boy's father but not the girl's - said their care had not been "deficient".
They said any troubling behaviour was more likely to be the result of the children's "confusing and damaging experience" of being in and out of care.
But a family court judge concluded that adoption is in the youngsters' best interests.
Detail has emerged in a written ruling following a hearing in Swindon County Court.
None of the family was identified but Judge Katharine Marshall said the local authority involved was Wiltshire Council.
Judge Marshall said the children were first taken into care three years ago after social workers became concerned about injuries the little girl - whose father is no longer involved with her mother and was not involved in the litigation - had suffered.
She said social workers were also concerned about the "basic parenting skills" of the mother and her partner.
The children had been placed with a foster carers for nearly two years while investigations were carried out.
Experts concluded that damage could have been caused accidentally or related to a viral infection.
And the judge said the children had been returned to their home in March 2013, with social workers providing support.
But in June 2013 doctors became concerned about "extensive bruising" on the little girl.
The children were taken into care again and returned to the same foster carers.
The judge said police had arrested the mother and her partner - but prosecutors had indicated that there was insufficient evidence to support a prosecution.
Social workers had told the court that the little girl had bruises on her face and leg which were "more likely to be inflicted that accidental".
They suggested that injuries had been inflicted by the mother or her partner - or were the result of neglect.
And they argued that both children "suffered significant emotional harm" when in the care of their mother and her partner between March and June 2013.
The mother and her partner argued that the girl's injuries were caused by "normal childhood play".
They said "rehabilitation" had been "going as expected" and said "behaviours displayed by the children" were "more likely to be attributable to this confusing and damaging experience" rather than to the "short period" in their care.
Judge Marshall said the "experience of being removed for a second time" had a "major impact" on the children.
She said evidence suggested that both had "struggled to understand what has happened to them" and were "at times bewildered and confused".
But the judge concluded that both would be at risk of harm if returned to their mother and her partner.
She approved the council's adoption plan - which would see the children remain with the carers who had been fostering them.
The judge concluded that the girl had suffered "significant physical and emotional harm and neglect" - and the boy "significant emotional harm and neglect" - when in the care of their mother and her partner.
Judge Marshall said: "I have no doubt that (they) are genuine in their love for both (children) and have tried to do their best taking into account their own limitations and parenting abilities, and more recently in the extremely difficult circumstances of the children having returned to their care after an extensive period in foster care where they received a very high level of care.
"However, the sad conclusion has to be reached that these parents could not cope, and are simply unable to manage parenting these children to a good enough standard where they would be safe in their care."