The article is about drone attacks in general, but the key paragraph reads as follows:
“Mr. Obama embraced a disputed method for counting civilian casualties that did little to box him in. It in effect counts all military-age males in a strike zone as combatants, according to several administration officials, unless there is explicit intelligence posthumously proving them innocent.”
In other words, if you’re a male who happens to live in a country at war with the U.S. (heck, even if the U.S. considers your country an ally), the U.S. reserves the right to kill you. Of course, if you’re innocent they’ll say “our bad,” kind of like women accused of witchcraft were let off if they didn’t float.