If you read the story your learn that Justice is in fact investigating a leak to the AP. The merits of such am investigation may be debated but for the AP to write this article in this fashion would be like a politician under investigation issuing a press release about the evil investigation against him. Everyone would understand it for what it is.
More important it is clear to anyone who understands what happens in this type of investigation that the Justice Department subpoenaed phone records. Those records came from the phone company not from AP. They relate to dates and times of phone calls not content. Under the law such a subpoena is perfectly proper and under the law Justice and the phone company must notify the party (in this case AP) that records were subpoenaed.
I think AP protests just a bit too much and seeks to smear Justice (knowing full well that many Republicans will jump on this quickly).
I think there's still a very live question of whether this was a prudent action on the part of the DOJ, as maximal restraint should always be used when subpoenaing journalistic records. But I do think he's at least on to something that such an article would definitely have included more and different context if AP weren't the party at issue and the 'secretly' phrasing does perhaps knowingly mislead.