Agnifilo noted that the situation involving Shkreli and Retrophin is "unusual" because Retrophin clearly wanted him to be prosecuted criminal after the company ousted him as CEO in 2014.
The lawyer said that Retrophin and MSMB shared a single computer server, but that their respective documents were on separate areas of the server, and protected by separate passwords.
Agnifilo said that he does not know how Retrophin obtained material relating to MSMB, but said, "they gave the government... MSMB material," in addition to Retrohin documents.
However, Agnifilo conceded that the defense does not know which, if any of those MSMB documents, might have been acquired by prosecutors through a source other than Retrophin. If the government separately acquired all such documents, it would mean Shkreli would not have a right to suppress them from being used at trial.
But Agnifilo met pushback on his argument from both prosecutors and the judge.
Mastumoto noted that Shkreli's contract with Retrophin required him to comply with company policies, and one of those policies was that employees did not have a right to privacy in their emails and other electronic communications on company computer systems. Matsumoto also questioned the idea of Shkreli having a right to the MSMB documents being kept out of the government's hands, as opposed to MSMB, as a corporate entity, having that right.
And Mastumoto also questioned why Shkreli had not removed the MSMB documents and taken them with him after he was ousted by Retrophin.
"He left them on the server," the judge said.
Assistant United States Attorney Alixandra Smith said that the claim that there were separate passwords and just one computer server for Retrophin and MSMB documents was not previously made in the defense's motion to suppress the MSMB evidence.
"This is the first time we're hearing this argument," Smith said.
Smith also noted that neither Shkreli, nor his lawyers, has submitted an affidavit attesting to the truth of the claim that there were separate passwords, and that in the more than one year since Shkreli was indicted, the defense has not identified any individual MSMB documents that had not been obtained by the government other than from Retrophin.
Smith said that Shkreli had routinely used his MSMB email address to conduct Retrophin business.
The defense will have time before trial to identify any specific documents it believes should be suppressed, and remount its argument about them.
The hearing came a week after Matsumoto granted Shkreli's request that he be tried separately from his former business lawyer Evan Greebel.
Matsumoto ruled that Shkreli's constitutional right to a fair trial would be at "serious risk" if he was tried alongside Greebel, particularly since Greebel's criminal defense attorney had threatened to act as "a second prosecutor" against Shkreli.
Shkreli, 34, will go on trial first, beginning June 26. Greebel, who also had asked for a separate trial, will be tried at a later date yet to be determined.
Greebel's lawyer Reed Brodsky had warned Matsumoto that if the two men were tried together, he would attack Shkreli as "a liar and a deceiver "who was guilty of both the charges in this case, as well as other uncharged crimes.
"We will be duty-bound to destroy Mr. Shkreli's credibility," Brodsky said at a prior hearing. "We are going to be an echo chamber with the government in terms of Mr. Shkreli's lies."
Shkreli refused to answer reporters' questions either on his way into the hearing, or as he walked out of it with his lawyers.
Clad in white pants, and a dress shirt, he dashed across the street outside the courthouse in downtown Brooklyn, and hopped into a yellow taxi cab after hailing it.
A courthouse worker, watching the scene, said, "You'd think with all his money, that guy would have a limo out here waiting for him."
Or at least, the worker said, "An Uber."