Another user on a different forum discovered a solution (which may not be ideal). Turn off iCloud Drive on the device that shouldn't get the call logs and the call logs will stop syncing. Thats the only solution that works, that I know of, so far.
Exactly what I said. iOS 9 is using iCloud to sync that information between devices. It's by design. sign out of icloud or use different Apple ID's on the devices and the issue resolves. With that said I would be more than happy to direct feedback that this is a not liked feature up the chain of command for you all.