There is a fundamental lack of understanding here on everyone's part, made worse by Trump's own misunderstanding.
The basis for the report:
That senior intelligence leaders appended/mentioned/referred to these allegations of Trump being compromised in a document briefing. The briefing itself was largely about Russian's involvement with the leaking of DNC emails.
The confusion from the Trump camp:
The allegation may only have been a footnote in the larger document and therefore not verbally communicated during the brief. Assuming Trump did not read the entirety of the report, he would deny it ever having been part of the actual brief (as he may only recall the conversation).
In his eyes, not only is the content false, but so is the basis of the report; that it was passed on to the POTUS and himself by the FBI.
The impact of James Clapper's statement
The statement was crucial as it was the first public acknowledgement that they did indeed "discuss" the document. This contradicts Trump surrogates who denied that the President-elect was made aware of these allegations by the Intelligence Community.
Trump does have a good argument.
CNN's justification that they merely reported on that the Intelligence Community notified Trump of these allegations does raise questions about journalistic ethics. Editors at CNN knew that it would immediately cast aspersions of the President-elect unfairly because there was no proof. But the lack of evidence would do little to soften the impact and tarnish his name even further.
Would they have published a report that President-elect Barack Obama was made aware of a dossier alleging he was actually born in Kenya, a dossier with no evidence? ​
No.
What CNN did isn't much different than Fox News bringing on a guest who makes statements about Obama's religion based only on hearsay.