Wanting to question the couple, they began searching for them and tried to reach them by cellphone without success.
The couple were found around 11 a.m. Sunday with the help of an anonymous citizen, police said. BART police officers detained the couple at the El Cerrito Del Norte BART Station until Napa Police could pick them up.
At a press conference Sunday afternoon a police spokeswoman said the the pair could face charges of special circumstances, making them eligible for the death penalty, or life without parole if convicted.
The Napa Valley Register reported that in recent months, police had visited Krueger's apartment several times for disturbances including late-night noise, slamming doors, and neighbors reporting possible physical abuse of Kayleigh, according to the property manager.
None of the officer visits resulted in an arrest, according to police.
Warner "moved in about 10 months ago and it all went downhill from there," said property manager Elizabeth Chechourka.
Police said there were "indications of past drug use and drug offenses" by Warner and Krueger, but did not give details.
Police officials said Napa officers had made several welfare checks at Krueger's home, most recently last week. However, it was unknown whether Napa County Child Protective Services had visited the apartment in response to any neighbors' complaints.
A woman who often babysat the three-year-old girl said Krueger raised Kayleigh alone after the child's father, Jason Slusher, was sent to San Quentin State Prison, according to the Register.
Staff Writer Clark Mason contributed to this report. You can reach Staff Writer Jamie Hansen at 521-5205 or firstname.lastname@example.org