(CNN) — Donald Trump’s attorneys have found a new reason to seek to delay the classified documents case: Some of the documents found in boxes at Mar-a-Lago have shifted out of order since FBI agents seized them two years ago.

Trump’s attorneys indicated in a filing Monday that the shuffling of documents within boxes in evidence also could be grounds for the case to be tossed. They said they would file a motion to dismiss if the prosecution “cannot prove in a reliable way how it seized and handled the key evidence in the case, which will be a central issue at any trial.”

In a brief order Monday, federal Judge Aileen Cannon paused the deadline the defendants faced this week for certain pretrial disclosures and said there would be a follow up order resetting pretrial deadlines and hearings. The order did not provide any further explanation.

Special counsel Jack Smith’s office acknowledged in a recent court filing that, in at least some of the boxes obtained in the Mar-a-Lago search, the documents are now in a different order within each box than when the Justice Department first took custody of the boxes.

“President Trump and counsel are deeply troubled to be learning of these facts approximately 11 months after the charges were filed in this case,” Trump’s attorneys wrote in the filing. The disclosures by Smith’s office “raise questions about the investigation and the handling of evidence that must be addressed before the matter proceeds.”

Trump was charged with mishandling national defense information after the FBI seized boxes in August 2022 from the Florida estate that contained documents with classified markings mixed in with other documents and personal effects of the former president. Trump and his co-defendants have pleaded not guilty.

The prosecutors noted in their court filing that the boxes have been subject to several reviews, including one sought by Trump. Cannon appointed a special master at Trump’s behest in 2022 to review the seized documents and determine what should be withheld from investigators because of privilege issues.

The order of the documents could become critical to the defense of Trump and his co-defendants. For now, defense lawyers are asking for delays, arguing the revelation has disrupted their trial preparations.

In Monday’s filing, Trump’s attorneys say they relied on the order of the classified material within the boxes when they reviewed them as part of the discovery process. At that point, the attorneys say the classified material was “buried within the boxes,” which they say could help clear Trump of any wrongdoing.

The attorneys also say “it was our understanding” that classified material was found next to items that “provided favorable context” around when the document was put in the box, according to the filing.

When the boxes were first seized in 2022, they were reviewed for privileged materials by a team of DOJ attorneys separate from the investigation team. Then, as part of another review by investigators, classified documents within the boxes were removed and swapped out with a placeholder sheet. And as part of the special master process ordered by Cannon, the boxes’ contents were scanned so that inventories of their contents could be created.

The filing from prosecutors said the documents and placeholder sheets stayed within the boxes they were found in, but that “there are some boxes where the order of items within that box is not the same as in the associated scans.”

Prosecutors acknowledged the discrepancy in response to a request last week from Trump co-defendant Walt Nauta that certain pre-trial deadlines be postponed.

The defendants had been required to tell the court by Thursday what classified materials they intend to use as part of their defense, but Nauta and Trump argued they couldn’t meet that deadline because of the evidence snafu.

Nauta has previously argued that prosecutors have not sufficiently shown that the boxes he is accused of moving out of a Mar-a-Lago storage room contained the classified documents sought by investigators in a May 2022 subpoena.

Special counsel Smith has argued that Nauta’s ability to meet this week’s deadline  – which Cannon has since removed – should not be affected by the fact that some of the documents have fallen out of order within each box.

A spokesperson from Smith’s office declined to comment further.

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