Both the White House and the CIA told NBC News that they don't comment on security clearances—but two sources who are reportedly privy to such information did. They tell the network that two "career White House security specialists" branded Jared Kushner's top secret clearance "unfavorable," meaning it would not be approved, after reviewing his FBI background check, but that they were overruled by Carl Kline, the director of the personnel security office in the Executive Office of the President. The sources claim Kushner's case wasn't an isolated one, with Kline overruling such decisions in the cases of more than 30 Trump administration officials. That volume is extremely atypical, the sources say, with just one rejection overruled in the three years prior to Kline taking the post in May 2017.
As for why the security specialists moved to reject Kushner's application, the sources gave some broad categories the FBI flagged: his family's business, his overseas contacts, his travel abroad, and meetings he held during the campaign. The NBC News piece gets more into Kushner's reportedly unsuccessful attempt to also seek an "SCI clearance" through the CIA, with a source saying that during the CIA's review, a CIA officer reached out to the White House security division, confused about how Kushner had secured even a top secret clearance. The Guardian writes the report "suggests new intrigue within the White House over the clearance process," a process that the House Oversight and Reform Committee this week announced it would be investigating. (The committee had said it would look into Kushner's clearance.)