Well, how was he supposed to know? The NYT hadn't published any stories about it.

"President Obama communicated with Hillary Rodham Clinton via email but didn’t know the “details” of how his secretary of state was using a private, off-the-books email address, the White House said Monday.

“They did have the occasion to email one another. … He was not aware of the details of how that email address and how that server had been set up or how Secretary Clinton and her team were planning to comply with the Federal Records Act,” White House press secretary Josh Earnest told reporters. “The president did email with Secretary Clinton. I assume he recognized the email he was emailing back to.”

It was revealed last week that Mrs. Clinton did not use an official government email address during her four years in charge of the State Department and conducted all business on a private account. The administration previously has said the president learned of the email scandal via news reports."

http://www.washingtontimes.com/news/2015...il-white-house/

Of course a clue to what was really going on might have been found in the fact her email didn't end in .gov, but, hey, Obama is an expert on the Constitution not computers.