Phillipos is accused of lying to federal agents and faces up to eight years in prison and a $250,000 fine if convicted.
He attended high school with the younger Tsarnaev at Cambridge Rindge and Latin School in Cambridge, Massachusetts, where they both live.
According to the court document, Phillipos hadn't seen or talked to Dzhokhar Tsarnaev for at least two months before the bombing. He was taking a semester off from UMass-Dartmouth and was only on campus the night of April 18 for a seminar.
The document says Phillipos' presence on campus that night is a case of "sheer coincidence and bad luck."
Phillipos was living with his mother, an Ethiopian who immigrated to the United States in the 1980s and is now employed as a social worker.
"Everyone knows Robel as being a compassionate, thoughtful and sociable person," his mother, Genet Bekele, said in an affidavit.
Previously, a friend described Phillipos as a good kid who took care of his mom.
James Turney told CNN affiliate WBZ: "Phillipos plays basketball and doesn't have 'any anti-American thing about him.'"
Kadyrbayev also remains in jail, awaiting a May 14 court date.
According to an FBI affidavit, Kadyrbayev had seen pictures of the suspects released by the FBI on April 18 and texted Dzhokhar Tsarnaev to tell him "he looked like the suspect on television." Tsarnaev texted back "lol" and added, "come to my room and take whatever you want."'
Attorney Stahl also said his client "did not have anything to do" with the bombings and disputed that he tried to block the investigation.
Kadyrbayev, a Kazakh national, was taken into custody along with Tazhayakov on April 20 on suspicion that he had violated the terms of his student visa, Stahl said.
According to an interview his father gave in April, Kadyrbayev, 19, "missed a couple, or maybe several classes."
"I can say about my son that he finished school with excellent grades; he was good at math. He helped others. When he saw that help was needed, he always accommodated," Murat Kadyrbayev told Tengi News and STV channel in Kazakhstan.
Kadyrbayev is not currently enrolled at the University of Massachusetts-Dartmouth.
He is charged with obstruction of justice and could face up to five years in prison and $250,000 in fines if found guilty.
Kazakhstan's foreign ministry said it was offering consular services to both Kadyrbayev and Tazhayakov. "We would like to emphasize that our citizens did not receive charges of involvement in the organization of the Boston Marathon bombings. They were charged with destroying evidence," the ministry said in a statement.