Apparently the boy's father was being investigated by Child Protective Services, and now police say it was a CPS worker who told them the father should be allowed to have the boy.
The boy's father showed up at League City police demanding officers help him get his son back. What happened afterward is raising a lot of questions.
"We let him down, that this happened. We're not gonna let this happen to him again," said Nancy Stout, Samuel's grandmother.
Nancy, 83, loves her grandson Samuel unconditionally.
"I've got lots of grandchildren, but he's the most interesting," said Nancy.
So when Samuel fled to her house for the third time, Nancy took him in. She says she knew about the problems between her son and grandson.
"He'll be fine as long as he's in a place where he will not gonna be harassed," said Nancy.
Stout's son, Neal Roberts, 49, has been convicted of an aggravated kidnapping in 1995 in Travis County, and a family violence assault in Galveston County in 1998.
So he when he showed up at Nancy's house to take his son, Nancy didn't want to let her grandson go. However, police said she had to. Their reasoning?
"It's the law. The father has the right," Nancy was told by the officers.
League City police says they called CPS and talked to the supervisor on duty.
"Well, the supervisor told them they could either release the child to the father or bring the child to us," said Estella Olguin of CPS.
However, according to League City police, CPS ordered the release of Samuel to his father. Police gave us this recording of the phone conversation between CPS and the sergeant called to the scene.
"I talked to the Harris County supervisor and she wanted me to call you back and let you know that the child has to be released to his father," said the CPS supervisor.
The officer replied, "Okay."
CPS responded to the recording in a statement saying, "This shouldn't have happened. There was a breakdown in communication between Harris County and Galveston County (CPS supervisors) and what was said to police obviously didn't give them a choice."
Wednesday's Amber Alert
Local police say a mistake by Child Protective Services was a factor in an Amber Alert issued Wednesday.
Samuel Kirtley, 14, was found late Wednesday night and the Amber Alert was canceled. Baytown police say Texas Rangers called around 10:20pm to say they recovered the boy in Weslaco. The teen had no obvious injuries. No new info was given with regards to the father, Neal Roberts.
Roberts was accused of taking his own son and authorities say he should not have been anywhere near the boy. Roberts and Kirtley had not been seen since Sunday.
Baytown police want to know why Roberts was allowed to take Kirtley on Sunday. They say a CPS supervisor is to blame. Roberts has two prior violent convictions for crimes against other family members.
On electronic boards across the state, the Amber Alert stared drivers in the face. The message was that the 14-year-old boy was believed to be in danger.
"We're very concerned about the child's safety," said Detective Alan Cliburn of the Baytown Police Department.
Baytown police issued the Amber Alert Wednesday afternoon. The child was last seen with Roberts Sunday, but he wasn't supposed to have custody.
"He was removed from the care of the father for a reason," said Det. Cliburn.
The whole story begins August 28 on the Fred Hartman Bridge. A deputy constable stopped Samuel as he was walking across. He said he planned to walk the entire 30 miles from Baytown to his grandmother's house in League City. He was seeking refuge.
"Basically he said he was trying to flee from his father's home, in Baytown due to physical abuse that was occurring," said Det. Cliburn.
Det. Cliburn says that's when CPS placed Samuel temporarily with his grandmother. On Sunday, Roberts, who according to police has prior convictions for assaulting a family member and kidnapping a child, went to get him and according to Baytown police, League City officers called CPS asking for direction.
"They informed them that dad was there attempting to gain custody, informed them about the open CPS case with the police department, but were given authorization by a CPS supervisor who said release the child to custody of the father," said Det. Cliburn.
Samuel hasn't been seen since.
A CPS spokeswoman couldn't address the allegations citing confidentiality laws, but did say in general, it's up to police officers in the field to make those decisions.
At the child's grandmother's house, Samuel's cousin didn't seem too concerned.
"Sammy has never complained about his father beating him," said cousin Timothy Fair.
However, fleeing 30 miles on foot over a bridge, Det. Cliburn believes is enough for them to take his abuse allegations and disappearance seriously.
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