Federal agents are preparing to scour roughly 650,000 emails contained on the laptop of former Rep. Anthony Weiner to see how many relate to a prior probe of Hillary Clinton’s email use, as metadata on the device suggests there may be thousands sent to or from the private server that the Democratic nominee used while she was secretary of state, according to people familiar with the matter…

The split within the Justice Department and FBI over Clinton-related matters has been particularly apparent in the bureau’s investigation of the Clinton Foundation, the Clintons’ family philanthropy. As the email investigation wound down in July, the internal disagreements surrounding the foundation probe heated up, according to people familiar with the matter.

New details show that senior law-enforcement officials repeatedly voiced skepticism of the strength of the evidence in that probe, sought to condense what was at times a sprawling cross-country effort, and, according to some people familiar with the matter, told agents to limit their pursuit of the case.

That led to frustrations among some investigators, who viewed FBI leadership as uninterested in probing the charity, these people said. Others involved disagreed sharply, defending FBI bosses and saying Mr. McCabe in particular was caught between an increasingly acrimonious fight for control between the Justice Department and FBI agents pursuing the Clinton Foundation case.