Mild spoilers.
Ellie is growing overtime to trust Joel less, and that's changing her behavior. That'll build more later.
At the end of last season, Joel and Ellie went to a hospital, did some stuff, then went back home unsatisfied. Joel told Ellie that there was no cure or anything she could help with. That hospital was a Firefly facility. The remaining few from that facility are now upset at them, to say the least.
I was also trying to remember the therapist connection... I think her husband got bit and Joel put him out of his misery, maybe? I could be off on that one.
Adding to that, game spoilers
In the game, we later see that she had gone back to SLC to get answers about what happened there due to those doubts, sometime between the events of the first and second game. Ellie confronts Joel and he confesses what actually happened.
They were beginning to repair things towards the start of the game, we later see through flashbacks.
They were beginning to repair things towards the start of the game, we later see through flashbacks.