"He was pressuring me and that's why we chose to leave," Kelsey Peterson told a judge Monday at a pretrial hearing.
U.S. Magistrate Judge F.A. Gossett denied Peterson bail, saying she was a flight risk.
Peterson said the boy left bruises on her arms and chest, told her what to wear and threatened her life. She said he was in a gang and had her name tattooed across his chest, and that the boy's family knew about and encouraged their relationship.
Lawyers for the boy said Peterson's allegations are not true and accused her attorney of lying about the boy and using Mexican stereotypes to cloud facts of the case.
"This whole case has been pulling things out of thin air and putting them forth as true," said Stu Dornan, a lawyer for the boy.
The teacher and the boy were found after a weeklong search led authorities to a mall parking lot in Mexicali , Mexico . Peterson pleaded not guilty Nov. 29 to charges of crossing a border to have sex with a minor.
The boy told The Associated Press after the pair were found that he and Peterson had sex. The AP previously named the boy as police searched for him but stopped using his name in reports after authorities charged Peterson with a sex crime.
Peterson, who has been fired from her job as a middle school teacher and basketball coach, said she left with her teenage lover after school officials started investigating their relationship. She hoped the rumors about them would blow over.
"I really thought it just might go away," said Peterson, who wore an orange jumpsuit and pulled back her hair in a braided ponytail. "And I know that sounds crazy, but that's what I thought."
But the school called police, and authorities including the FBI started hunting for the pair.
Peterson wept after being denied bail, and looked toward her family seated at the back of the courtroom as a U.S. marshal shackled her wrists after the hearing.
Peterson's lawyer, James Martin Davis, has said the boy is not 13 years old, has a 2-year-old child of his own and was Peterson's pursuer, not her victim. He said he would try to negotiate a plea deal with prosecutors before a Jan. 22 hearing.
A birth certificate provided to the AP earlier by the officer who arrested Peterson said the boy was 13. The officer said he got the certificate from the FBI and it was recognized by the Mexican government. Lawyers for the boy said Monday that the government has verified his age to them.
But Davis said the certificate was provided by the boy's mother - also an illegal immigrant - and should not be trusted because it could be counterfeit.
The boy's age would not affect the current charges unless the defense established the boy was 18 or older. But it would make a difference if prosecutors end up charging Peterson with statutory rape because Nebraska's age of consent is 16.
The discovery of the submarine has unveiled a few "inconsistencies." For example, how can one explain the fact that the sub was found where it needed to be searched for from the start?