In a court filing, James' lawyers argue that FBI agents took oral DNA samples from Frank James without informing his legal team.
They also say he was improperly questioned in his jail cell and claim agents had him sign several documents.
James, 62, is accused of setting off smoke grenades and firing a handgun 33 times inside a crowded subway train on April 12.
James was allegedly wearing a surgical mask, a construction helmet, and a safety vest when he opened fire inside a Manhattan-bound N train in Sunset Park.
Ten people were shot.
The NYPD found a Glock 17 9mm handgun with three extended magazines and a U-Haul key at the scene after the mass shooting. The gun was allegedly purchased by James in 2011 in Ohio.
Police said that they identified James by using video from prior to the shooting showing him entering the Kings Highway subway station using a black cart that was later recovered at the scene of the crime. They also recovered James' orange jacket as well as the construction helmet he was wearing.
James was arrested near St. Mark's and First Avenue without incident. He didn’t respond to reporters shouting questions as police escorted him to a car a few hours after his arrest.
The NYPD got a tip Wednesday that James was in a McDonald's in Manhattan's East Village neighborhood, according to Chief of Department Kenneth Corey.
The tipster was James, and he told authorities to come and get him, two law enforcement officials said. They weren’t authorized to discuss the ongoing investigation and spoke on condition of anonymity.
James was gone when officers arrived, but they soon spotted him on a busy corner nearby.
Four police cars zoomed around a corner, officers leaped out and, soon, a compliant James was in handcuffs as a crowd of people looked on, witness Aleksei Korobow said.
The U.S. Attorney's Office released a statement saying the claims that James had his rights violated are inaccurate and his constitutional rights were not violated.