Whaley is feeling a ton of pressure right now, I think. He's been in his position for a few years. He has a new owner, that tried to hire a head of football operations guy a few months ago. Now he has a larger than life personality head coach in Rex Ryan. On top of it he has someone in the organization leaking bits about him to the media. Hes not in a comfortable position. I think Whaley is probably trying to assert his dominance against these factors. He knows he is under a microscope, and I don't expect its going to get much better for him.
He knows the Bills need to win now, or he will be under a lot of scrutiny after this season. So of course there's going to be some disagreements behind closed doors, but that's where they need to stay, behind closed doors. The fact that this stuff was leaked doesn't make Whaley look as bad as it does the organizational structure. Winning will cure that, but as we all know, it comes down to QB. Whaley has built a great roster, but without a legit QB, we all know what happens. So to Whaley, and the org, Twitter is not their friend. And won't be until they win.
I would expect Pegula is, right now, as we speak, shopping for GM's. And this season will be a gauge of whether he needs one or not.