I imagine they presumed that due to the Guardian paying for the flights, and Guardian lawyers being involved in trying to resolve the detention. It seems that while he is working with/for the Guardian in some paid capacity, "employee" is probably not the correct word for the relationship.
We could ask the NSA for verification I guess but there is no mention anywhere on the Guardian sites or elsewhere that he's an employee so it is possible this is indeed mistaken.
Paying for a ticket != signing an employment contract. That doesn't mean there is no such thing. I'd assume that the people that wrote that had some more information than what's in the media elsewhere but still it is as of yet unverified. And it would make a serious difference in this case.