A woman who was subsequently killed by her partner tried to cover up for him when he accidentally shot their child with an air rifle, a court heard.
Doctors became suspicious of an explanation given by Kelly Franklin for her child's eye injury.
Ms Franklin, 29, was allegedly murdered by the child's father, Torbjorn Kettlewell, last August.
A jury at Teesside Crown Court heard the child was injured in May 2017.
Kettlewell was cleaning the unloaded weapon when he accidentally discharged a blast of air from it into the child's face.
The incident led to social worker Emma Deacon becoming involved with the family.
"I'm not aware what Kelly told the nurse," said Ms Deacon. "But her account did not match with the injuries suffered by the child.
"It became apparent that I couldn't always rely on Kelly when she was talking about Torbjorn Kettlewell and their relationship."
Social workers decided to remove all three children from the family, placing them first with relatives then with foster parents.
"When we went to take the children we found clothing all over the floor," said Ms Deacon.
"It wasn't possible to work out what was clean and what was not, so we had to buy new clothes for the children to go away in.
"The police wanted to give the children something to eat while they were waiting, but no food could be found in the house."
Ms Deacon said one of the children had educational and other problems, but his condition improved markedly while he was in foster care.
Kettlewell was not allowed unsupervised contact with the children after splitting from Ms Franklin in late 2017.
He was trying to get back with her in August, last year, when he is alleged to have murdered her in Oxford Road, Hartelpool, not far from their former home Kipling Road.
Under cross-examination from Richard Wright, QC, for Kettlewell, Ms Deacon agreed the couple's relationship was 'dysfunctional, but there was a real intensity about it'.
Kettlewell is jointly charged with Julie Wass, a neighbour with whom he was having an affair.
Ms Deacon told the court that about three weeks before the killing, she received a call from Wass to say Ms Franklin was taking drugs so should not be allowed to have the children back.
The court heard Ms Franklin took and passed a random drugs test.
Detective Constable Robert Griffiths, a digital media investigator with Cleveland Police, told the court there was a series of 'highly sexualised' messages between Wass and Kettlewell which were found on a mobile phone linked to Kettlewell.
Police recovered an iPhone from Wass, but were unable to recover messages from it.
"It had an app on it called Wickr," said Det Con Griffiths.
"That is a highly secure encryption messaging app which can be set to delete messages once they have been read.
"Once deleted, there is no way of recovering the messages because they are not stored anywhere.
"The only other time I've heard of Wickr being used is among the higher levels of criminality."
Kettlewell, 30, of Oval Grange, Hartlepool, denies murder on August 3.
Wass, 48, of Kipling Road, Hartlepool, denies murder.
She admits assisting an offender.
The case continues.