A post-mortem found the teenager died before the blaze, Chenango County District Attorney Joseph McBride said last week.
The fire was reported around 1.15am on March 1 at the family’s home in Mount Upton, New York state.
When police arrived at the scene, Ernest Franklin reportedly pointed to the room where his son lay dead.
He told officials that he was away from the house chasing down the family’s dogs when the fire started.
Heather Franklin claimed to have been driving around from 11.30pm until about 2.30am, according to the report.
WBNG-TV reports that McBride said during the hearing that the victim was badly burned. “Because of the damage to the body by the fire, the pathologist is not able to determine the cause of death,” the attorney said.
The autopsy, though, showed Jeffrey Franklin had died before the fire, according to McBride.
According to the report, Heather Franklin’s attorney told the court that she is innocent until proven guilty.
Her husband’s public defender said it is unclear if the movie was relevant to the event and said his office has hired a forensic pathologist to investigate. ‘Manchester by the Sea’ stars Casey Affleck as a grief-stricken man who, it is revealed through flashbacks, accidentally killed his children in a fire while under the influence of multiple substances.
The movie scored two Oscars from six nominations, including a best actor win for Affleck.
The Franklins are charged with murder, arson, and tampering with physical evidence.