This scene bothers me so much

Not even the worst of Jack's moments. Anyway...

Your idea, Jack. Not Will's. Abigail in Minnesota was the opinion that best served YOUR agenda.

Do you remember that?

Not happy, after almost placing a death's fault in Will's hands, he starts complaining that Will's profile of the killer wasn't exactly right.

Where the fuck was trained this man? Does he really think that a killer's profile is 100% accurate?    

First fucking doubt Will has about himself.

He is wrong, it's true -well, Hannibal knew exactly what to do to fuck up the investigation- but it doesn't matter. Will doesn't know that and the moment Jack yells, he doubts.

Hannibal tries to mediate.

There! Jack just wants his idea of Abigail Hobbs to be true. And he wants to listen to Will saying that he is right. That's all he wants.

Will contradicts his idea.

Jack keeps pretending to give a fuck about what Will thinks about Abigail.

Will turns to look at Hannibal! I can't find any other explanations if not that he is tired of Jack's questions and he doesn't know what to do.

Will shouldn't feel guilty of anything, he sure doesn't need to feel guilty for thinking that Abigail is innocent... And he still does!

He looks for Hannibal's support -this is so sweet, Will hasn't known Hannibal for a very long time and this is a demonstration of trust.

It's like Will is saying

Help me, you know Abigail, we know Abigail, tell him.  

And Hannibal can't help it. He is already tired of Jack. When he will try to alienate Will from Jack he won't do it just for his agenda or for his fun. Jack is not Will's friend. To keep Will away from Jack would be an act of kindness.

In other words 

Are you a fucking idiot and just think that Abigail is not involved because you want to?

Since Jack is the one that chose Will to be in the field and to help with the crimes, it’s a little too early to doubt about his empathy. The funny thing is that Jack is completely right and he manages to be a fucking asshole anyway.

Hannibal can't shut up, I understand.

As in “Are you done?”

Like he is scolding him.

And Jack:

LOOK.

He says LOOK.

Like... Don't defend him, he is a bad guy I need him to know he is not as trusted as he thinks.

I mean, in an instant it becomes fucking Will's trial.

Jack is always looking for someone to blame. I can’t stand him.  

Some of the insecurities Will experiences during the season are Jack’s fault.

And when Jack sends Hannibal away to escort Abigail out of Minnesota and asks Will to stay there with him, Hannibal casts a last look to Will like he is not happy to leave him with Jack.

Hannibal has already  his agenda and he has already planned killings and people to blame, but I think that glance is genuinely concerned. He knows he is not the only one who plays with Will’s mental health.