NEW YORK (CBSNewYork) — Questions are being raised in the death of a 6-year-old Harlem boy about whether the city failed to protect him by missing crucial warning signs.

Zymere Perkins died Monday. Prosecutors said Wednesday night that a preliminary autopsy showed Zymere had several broken ribs, old injuries and was severely malnourished.

Neighbors said they saw the warning signs.

“It was just bruises on top of bruises. It was all bruises,” Joanne Martinez said. “It was all bruises.”

Neighbors said authorities knew about them as well.

“It’s been multiple time that they’ve been here,” said neighbor Joe Moore.

The little boy’s mother, 26-year-old Geraldine Perkins, and her 42-year-old boyfriend, Ryshein Smith, were arraigned Wednesday night on charges in connection with his death.

Court documents say early Monday, Smith allegedly beat the little boy with a broom stick until he was limp.  Police sources say he also held the boy’s head under water in the shower.

Perkins told police she was there during the assault, but prosecutors say she never called 911 and hospital staff believe the boy had been dead for several hours before Perkins brought him in.

Her family defended Perkins on Wednesday.

“Geraldine Perkins, my niece, is innocent,” one woman said,

When asked about Zymere’s death Wednesday, Mayor Bill de Blasio called it “incredibly troubling.”

“What I think I can safely say is that there were warning signs, they were clearly looked at by a variety of agencies. How that didn’t lead to a different outcome is what I don’t understand and I find it an unacceptable outcome,” he said.

While the mayor said he wasn’t going to speculate on the case, he said a full investigation is needed.

“What I want to know is if agencies were involved with this child, whether it’s NYPD, Department of Education, ACS — I want to know what happened and why,” he said. “If we find anything that was done wrong, we’re going to fix it immediately because this is unacceptable.”

A June 16 audit by Comptroller Scott Stringer found that the ACS was putting thousands of children at risk because of, “shoddy investigations and poor oversight.”

ACS said it is investigating the Perkins case with the NYPD and has 60 days to complete the investigation.

The medical examiner has not released the cause of death in this case.