Early in President Donald Trump’s term, when White House officials heard him complain vociferously about Amazon.com Inc. they arranged private briefings in the Oval Office to make sure that he would talk knowledgeably about the company.

Gary Cohn, his top economic adviser, and other officials gave PowerPoint presentations and briefing papers they believed debunked his concerns that Amazon was dodging taxes and exploiting the U.S. Postal Service.

It...