Right now everyone is assuming there's only one Sphene that we've met. Yet, after reading a friend's thoughts about Sphene being upset about Zoraal ja using up the souls I started to wonder if we are sure there isn't two Sphenes. Heck right before I fought her as Queen Eternal it had made me think of the fight against Adel in FF VIII. Though during the Queen Eternal fight we never once had to worry about the health bar of the smaller Sphene in the middle of her chest. Unlike with the Adel fight where you had to make sure Rinoa didn't die or you'd get a game over screen.
We know that the devs don't give us parallels to other games in the franchise for no reason. In VIII sorceress can possess people including other sorceress. Where they're unable to act freely of their own. So what if we had a Sphene that was trying to fight the version of Sphene that Queen Eternal was? A Sphene that would have let Cahcuia find out a way to overide one of those floating bot's programming and send it outside of Living Memory. After all we are sent to the resistance by Sphene.
Then there's all the times she's about to spill the beans, but doesn't due to other security robots wandering nearby. Along with one of the last times we talk to her where she says something to us that was heavily distorted. It's the last memory we think of right before our fight with Queen Eternal. Why would she be worried about the security robots listening in on a conversation with us if they technically are her? Sure, at the time these talks happen the game wants us to think that Zoraal ja is listening to everything that they pick up when Sphene isn't "possessing" one. But what if that wasn't the entire reason why she'd stop herself from continuing on and nervously laugh while trying to change the subject.
What if that Sphene wanted us to destroy Queen Eternal so that she could finally go against that version of herself programming? Maybe Queen Eternal's programming is all Preservation's doing and the other Sphene is something that Krile's parents organization tried to accomplish but had to opt for a different plan due to something in their coding that made one overide the other?