This morning:
Why Trump is confused: As Axios detailed in Trump 101, the president reads the Times in print. He's seeing their front page today, which has that quote.
But... The NYTimes story he is reading this morning was published before 9pm last night, while the White House released the details of the call around 11pm. The Times has since updated their story to reflect his phone call, which Trump would see if he read them online.