The first sentence reported the US DOD said the flight was OVER the islet(s).  The second sentence reported the USAF said they didn't fly NEAR the islet(s). 

When there are two units reporting, which one has the higher authority?  The higher hierachical one.  This whole story came out of the DOD first, essentially the US DOD said, "this time we are not only NEAR the islet(s), we are OVER the islet(s)".  The questions is then - "There are many, many islets in the South China Sea claimed by China, which one(s) they are talking about?"  Apparently it was not one of 永暑礁, 渚碧礁, 美济礁, or 西沙永兴岛,  otherwise the results would be very serious.  Then which one(s) the US DOD is referring to?

The US is playing the game of inching forward.  Each time they inch forward a little bit, a little bit, until China starts to respond seriuously.  Each time they humiliates China a little bit, although you can say, superficially.  But it's an open humiliation all right in front of the whole world.  This process won't stop until a serious incident erupts.  It doesn't look like the whole thing will end well.  We'll have to wait and see the eventuality.  But I can say for sure, it won't be pretty.