I think the issue is two-fold.
First, you may have been soaking it for too long. That one is kind of obvious in hindsight given what happened.
Second, the SuperStones can swell in weird ways even if they are only soaked for brief periods. I started
a thread about this a few years ago. If you look at the photos, you will see that the swelling is not uniform along the entire length of the hone. When you have variable swelling in one hone glued to another hone that is also experiencing variable swelling there is going to be some tension between them. I suspect this is what happened.
I think the only prevention for this is to keep soaking times to a minimum. Of course that doesn't help in your case. If they were mine, and I could not get them replaced, I would try to finish the job and get them separated completely with more soaking and dental floss.