It's not like CDP likes to explain important plot ploints anyway. Even after 2 playthrought I'm still not sure what Eredin actually wanted from Ciri. At least not in a way that is logical.
It's not like that is any good excuse in the first place. The lacking writing of CDPR is the prime reason why we talk about the topic here.
But the reason why she doesn't trust Yennefer 100% is sufficiently explained imo. You just have to add together several conversations and behaviors.
The conversation between Phillipa and Geralt in the sunstone cave. The conversation between Ciri and Yennefer on the boat and the conversation between Ciri and Geralt outside of Novigrad. Furthermore the (from my point of view) rather confidiental behavior between Emhyr and Yennefer, at least too confidiental for two rather secretive characters like the emperor and the sorceress. Though spending more than 6 months together probably had some impact.
So I still have no idea about why there is distrust between Ciri and Yen from the very beginning. You care to explain?
The only possible reason is Yen's collaboration with Emhyr but it's nowhere explained that Yen had some secret agenda beyond just finding Ciri. And if anything, Ciri should blame Geralt for the very same thing...
And the cave? That's just some wild theories by Philippa. Nothing of that is true. On the opposite, if you romance Yen in TW3 she offers to Geralt just before the end to leave all politics and just settle down with him somewhere. That is a clear contradictin to Philippa's theories in the sunstone cave. It's all just bullshit imo. And if Ciri had just some basic brains and emotional maturity she'd know that...
It's extremely unlikely that Yen would ever do anything to harm Ciri. May I remember you that her mother complex is her major driving force. She would do everything for her child. No force - especially not Emhyr - could change that. If Ciri believes that Yen could somehow turn on her she's either extremely stupid and ungrateful or something really serious must have happened between them - something that isn't shown or even indicated in the game. It's imo just bad characterization. Ciri is a badly written character in TW3, basically a spoilt egoistic brat without any real depth...
uch:
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Ok, they lived in the city and Geralt hated it. What else? When he got sick of it , he just left her without a single word - instead of, I dunno, talking about a problem like an adult.
You can't "talk like an adult" to Yen. She doesn't make compromises. Either Geralt agrees with that or Yen gets furious, sometimes in such intensity that it's a danger for health and life. Geralt knows that quite well and he says in great clarity several times in the books. That's the point. She does whatever she thinks is good. Period.