Perhaps, but it is what it is. I mean, that's the one part of it all that isn't speculation, since it's spelled out in the CI.
If Nerv didn't do it on purpose, it must have been a conscious choice by Kyoko. Besides, why should a contact experiment alone divide a soul? I find deliberate soul division a lot easier to believe that an Eva's core just deciding to vacuum up part of a soul for no particular reason. Why didn't the entire soul transfer over?
We're told explicitly in the show that Kyoko's CE was a failure, and in the CI that her soul was torn in half as a result. Deliberate soul division just isn't in the cards in her case since it's directly contradicted in multiple canonical sources.
As to why it failed the way it did: I can only assume she was trying to improve on Yui's attempt, and was only partially successful. My suggestion here is merely that Rei's attempt was yet another effort to improve on Yui's effort, and that it worked out better than Kyoko's did.
It's a lot easier to handle if you assume no one ever does it deliberately and that Nerv barely knows what they're doing -- they just throw shit at cores and hope something sticks.