Learn a different Behavior!

We have adopted to littermate kittens and they both used the same litter box.
Months later we got an automatic cleaner litter box and works great for 1 cat
and not so great for the other. The OTHER cat goes #1 in there, but goes #2
in discrete little places around the litter box and around the same room. We
are at a loss as of what to do. I've tried "pet repellent" spray in the
places she keeps going. That doesn't seem to work cause she finds another
spot in the room. Any ideas, thoughts, concerns?