Any time she is able to detect something weird about a person/object (or they detect something weird about her):
The Shapeshifter disguised as Dipper in Familiarity,
Dipper after he turns into a girl
Freaked out by the Stone.
Bill says there's something different about her
Mina really didn't like her
Whenever something happens to her that would result in a normal person being seriously wounded or killed, or doing humanly impossible things:
Not being hurt after Shapeshifter throws her through a window
Beating a rock golem in a staring contest (and breaking the record in the process)
Not really hurt by being hit with a cabinet or getting a large splinter in her back
Not passing out when hit with a tranq dart
Then there's how she acts around other people- ie, avoiding them as much as possible:
She mentions loosing friends early on
She freaks out when Tambry shows up
She goes out of her way to avoid going into town while Mabel is a werewolf
Then when she goes into town for the Duskhope concert, she's hiding in her jacket (and not sweating despite the heat) and shuts down when it is revealed that Robbie is in the band.
Among several other things, like not being on Yuki's list of robots, or her reacting to the news that a phoenix can revive the dead and crying when it dies.
Omir working with the Warlock:
The weird looks the Warlock gives him
When he has an umbrella in Ashes in the Sky when most of the town doesn't expect a storm
Him always telling people to leave town
And a hooded person walking with him the day after the Warlock escapes jail
Zander being the Guardsman:
The code about gardening
His string theory wall with a lot of info no random musician would have
The song Gaiatale being about the Paths
Arline recognizing him and his comments the she still has stuff to learn
And whenever one of them shows up, the other doesn't. They are never together.
