Montell Figgens, a lawyer for Thomas, told The Associated Press both guards are being "scapegoated."
"We feel this a rush to judgment by the U.S. attorney's office," he said. "They're going after the low man on the totem pole here."
U.S. Attorney General William Barr vowed earlier this year to investigate Epstein's death and some "serious irregularities" in his treatment at MCC. In August, Barr announced the acting director of the Bureau of Prisons had been replaced and reassigned.
Epstein died weeks after an earlier suicide attempt, according to investigators. Officers found him with a strip of bedsheet around his neck in July after he apparently tried to hang himself, authorities said in the indictment unsealed Tuesday.
Officials briefly placed Epstein on suicide watch after the July suicide attempt, though that status had been lifted before Epstein's suicide in August.
Epstein had been housed at MCC since his arrest in July on federal sex trafficking charges. He had been accused of sexually abusing and exploiting dozens of girls as young as age 14 between 2002 and 2005.
He had pleaded not guilty and was preparing to argue that he could not be charged because of a 2008 deal he made to avoid federal prosecution on similar allegations in Florida.
Epstein's death prompted a whirl of conspiracy theories from people, including members of Epstein's family and some of his alleged victims, who questioned whether it was possible that he'd killed himself in such a high-security setting. His death was considered a major embarrassment for the Bureau of Prisons, according to the AP.
The Associated Press contributed to this report.