Whitaker might not be fully tuned in to what Mueller has, so when Trump and the WH called him raging about the BuzzFeed report, knowing it's true and wanting to fire Mueller, Whitaker went to Rod and asked him if it's true. Rod in an effort to protect the investigation told Mueller to put out the denial, but word it carefully, so it's not a blanket denial of the story, but could be interpreted as just small details being wrong, so when it's proven true later, the statement can't be used against Mueller.
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