The girl's body was found Feb. 1 on a bed in the couple's apartment at 2060 Wilkins Ave. in Napa when police went to check on her welfare.
Police said Kayleigh's body had been put in a suitcase and placed in a freezer.
Lieberstein said an autopsy confirmed the girl died from "multiple blunt impact from injuries to the head, torso and extremities due to fatal child abuse and neglect."
Krueger, 23, and Warner, 26, each face 25 years to life in prison on two charges each -- murder with malice aforethought and assault on a child producing great bodily injuring causing death.
They will return to Napa County Superior Court on April 2 for setting of a preliminary hearing. Both are being held under no bail in the Napa County Detention Center.
Krueger and Warner were seen leaving the apartment with luggage on Feb. 1. Neither had a car and efforts to contact them by phone were unsuccessful, police said.
After information about the couple was released to the media, police received an anonymous tip from someone who saw them at a restaurant in El Cerrito on Feb. 2, police said.
BART police detained Krueger and Warner at the El Cerrito del Norte BART station. Napa police responded, interviewed the couple and arrested them.
Napa police Capt Jeff Troendly said police went to the apartment on Jan. 29 after someone called to express concerns that Krueger was under the influence of drugs, was not feeding her daughter and was allowing anybody to stay at the apartment.
Police found no signs Krueger was under the influence or that Kayleigh was in danger, Troendly said.
Between June 2012 and Feb 1, there were 14 calls for service at the apartment, Troendly said.
The calls were about unwanted or suspicious people at the apartment, vandalism, petty theft and harassing phone calls but not for violence, he said.