Doesn't that kind of make sense considering Kira's reaction to Helena or knowing that Alison wasn't her mother in the first season? Maybe there was something about why Sarah is Fertile that is allowing Kira to be this way.
Psychic powers never make sense. People assume that just because other people can perceive things they can't, that there must be something mystical about it. Usually it's just a matter of being really perceptive and observant. Fraudulent psychics read people the same way Sherlock Holmes did, by observation of clues and behavioral responses that most people aren't trained to recognize. Kira's perceptions could easily have been explained the same way. It's the same with the way animals have perceptions that some people misread as "psychic." It's nothing of the kind -- it's just that animals are more attuned to body language, scent, tone of voice, and the like, things that we tend to overlook because we focus more on the spoken word.
And it's not really that hard to believe that a child could distinguish her own mother from an identical twin. After all, she sees her mother every day, knows her behavior and personality. She could probably have distinguished Alison's scent from Sarah's as well, since they probably use different bath and hygiene products. Someone else might confuse the two based on their identical appearance, but I suspect any child could've distinguished her own mother from a lookalike who'd never met her before. Children are still learning, still observing the world carefully and open to new things, whereas adults get complacent in their assumptions and are more easily fooled.
So until this season, nothing about Kira's perceptions required her to be anything more than a highly intelligent and observant person, or perhaps someone with unusually acute senses. What she knew could've been discerned from direct observation of people. Knowing what they're feeling from a distance, though, is much harder to justify.
I wasn't a fan of the Sarah being a jerk scenes though, even though she did have a right to be suspicious. While I like Felix going on their own, I miss that dynamic of the group working together. I get they were trying to instill some conflict between them this season but for some reason it's making me really uncomfortable.
It's not pleasant to see, but it's understandable. Going through all this ordeal would undoubtedly be hard on Sarah. She's been running scared for six months now, having her whole worldview overturned, trying to deal with this Vast Conspiracy and protect her daughter, being surrounded by death. Most TV characters can go through an endless string of traumas and still be okay, but realistically, it would take a terrible toll on a person, and I think we're seeing that in Sarah. She's always been a grifter and a scavenger, so trust doesn't come easily to her, and she has good reason to be paranoid now. So maybe she took it a little too far.
And on Felix's side, he's reacting to the discovery that Mrs. S is Sarah's biological kin, which has thrown his own status as an orphan and foster son into relief. He's grown up believing he and Sarah were bonded by their mutual lack of biological family, and now Sarah's related to at least half the people in their life while Felix is still alone. It's understandable that he'd resent that on some level, that he'd feel cast adrift and want to find some new connection. If not for that, he probably would've been more understanding of Sarah's efforts to look out for him, but with the tension he feels now, it felt like an affront, like Sarah was trying to take away the one biological connection he'd managed to find.
Come to think of it, that seems to be a recurring theme this season -- the yearning for a biological connection. Alison and Donnie envy Helena for being pregnant. Brightborn attracts and exploits infertile clients who yearn to conceive their own children.