Arguments the government offered behind closed doors when seeking a search warrant in the investigation of Hillary Clinton's emails are causing alarm among some transparency proponents and civil liberties advocates.

An affidavit unsealed Tuesday by a federal judge in New York shows that the FBI claimed there was probable cause to believe that a laptop belonging to Anthony Weiner, the estranged husband of top Clinton aide Huma Abedin, contained evidence of crimes involving illegal possession of classified information.

Clinton aides and others have vigorously disputed that assertion, but critics are also zeroing in on another aspect of the warrant application: a claim that the Clinton-related emails on the laptop were likely to contain "contraband, fruits of crime or other items illegally possessed."

Another passage in the affidavit seems to assert that classified information remains the government's property, no matter where it exists: "There is … probable cause to believe that the correspondence … on the subject laptop contains classified information which was produced by and is owned by the U.S. Government."

Some experts say the FBI affidavit, which almost certainly was vetted by Justice Department prosecutors, appears to argue that the government has the right to seize any information it deems classified from any place it has reason to think such information may be.

"This has implications that are terrifying and unacceptable," said Steven Aftergood of the Federation of American Scientists. "We haven't seen this line of argument widely pursued. … Taken literally, this would mean the end of independent reporting on national security policy."

Some of the concerns and fears stem from the fact that nearly all the information on Clinton's server that the government now asserts is or was classified was not marked classified at the time. So, it's not that the feds are arguing that the Weiner laptop was likely to contain actual classified documents that were stolen or copied in digital form, but that the topics or facts discussed in the messages are classified.

One former federal magistrate said he found the language in the affidavit confusing when it mentioned government-owned classified information.

"I am not sure what probable cause of correspondence that 'contains classified information which was produced by and is owned by the U.S. Government' means," said Brian Owsley, now a law professor at the University of North Texas. "It does not support a finding of probable cause of a violation of [the Espionage Act.] Moreover, the affidavit and the government do not allege a violation of any other federal criminal statute."

"It does not seem to advance the finding of probable cause regarding the statute at issue," Owsley added.

Another layer of complexity is that no law makes it illegal to possess "classified information." The Espionage Act refers instead to national defense information, which is potentially open to much broader interpretation, but has been narrowed by the courts. One such ruling also said the government had to meet a much higher burden of proof when the information wasn't marked as classified.