Yes, Claire did still have three wishes left ... but now Olivia was also, essentially, the genie's master as well. So, even though she wasn't mentally present at the moment, Olivia would be granted five wishes of her own. But as it turned out, it didn't matter when Genie could grant her wishes. She could, in fact, grant them right now. And Genie was powerful enough to encourage Olivia to make her wishes known, even if Claire was in control of her body.
So what should Genie do? Allow Olivia to make some or all of her wishes first? Or let Claire finish off her three remaining wishes, and grant Olivia's wishes later?