So I've finished the game once, but second time around after killing Kellogg Doctor Amari refuses to see me. Instead of being downstairs she's on the ground floor and says she's busy. I have Kellogg's brain. Anyone experienced this bug and know how to fix it?

I would assume you have talked to Nick about the issue? He does say he needs to introduce you to the Doctor.

Yeah so the first time around I was using Nick as a companion and after the mission he suggested going to Amari when we went to his office. This time around I started with Cait as a partner from combat zone. This is the only variable I can think of in addition to doing the mission at a lower level. I even redid the mission where I kill Kellogg with Piper and Nick, just to make sure it wasn't the companion causing an issue.