I'm guessing the reason that some of the FBI agents did not believe there was probable cause for the Mar a Lago raid is because previously, when the agents were at Mar a Lago, they had told Trump it was acceptable for him to keep whatever documents were in his possession, as long as he kept them properly secured, until the dispute with the National Archives (note: that's a civil dispute not a criminal dispute) as to proper disposition of the documents had been resolved.

Even if the agents who had given Trump permission to retain the documents were legally incorrect to do so, Trump's good faith reliance on those representations negates any mens rea.

A warrant requires probable cause that evidence of a crime might be located in the place searched with reasonable specificity as to the location and the nature of the evidence sought.

However, it is not a crime to retain documents with the express permission of the federal agents who are specifically in charge of the custody of those documents, which Trump had.

Without looking at the warrant application one cannot know whether the information provided to Judge Cannon in the affidavit(s) advised the court that Trump had been given permission to retain the documents.