* Random Apple engineer finds the implant.
* Goes directly to FBI without telling boss at Apple.
* FBI gags the engineer, says "Do not even tell your boss about this, it's national security and we're handling it".
* Bloomberg catches wind of this (maybe the same engineer leaks to them?), publishes their story.
* Engineer is now freaked, goes back to FBI and says "Are you really sure I shouldn't tell by boss?" and they say "Yes, we're sure, you are legally bound to secrecy".
I don't know how security teams, the FBI, or national security work. But that's the only scenario that comes to my mind which would explain both sides being completely sure of their version of the story.