02:“Evangelion Unit 01 has become an absolute being!”
Mbryo: Seele seems to know that Unit 01 already possessed the Fruit of Knowledge, which is why they are so alarmed about her gaining the Fruit of Life through the incident in Episode 19; they know that she's now capable of achieving a level of existence equal to that of god by having both Fruits. Which raises a question: why does Unit 01 have the Fruit of Knowledge in the first place? The fact that Seele had no qualms about installing the S2 Engine in Unit 04 or the MP Evas shows that 'normal' Eva units, the ones cloned from Adam, do not normally possess both fruits. This implies that simply possessing the soul of a Lilin is not enough to grant an Evangelion the Fruit of Knowledge. So where did Unit 01 gain hers? Did she inherit one from Lilith?
Dr. Nick: I would assume it's simply a matter of Yui being an active resident soul who went in willingly and knows what she's doing. She's able to reason, plan ahead and apply her knowledge, whereas the other poor souls in other cores are trapped and mostly dormant. Even if they're able to exert their will, as in the (admittedly very special) case of Unit-00, it's just blindly lashing out; momentarily destructive, but not a threat to Seele's plans.
