I'll add my name to the list of those experiencing this; but not just in iOS9. I can't say for sure but probably since 8.2 or 8.3 (but no issue with text messages).
I've checked everything, literally. Each iPhone is only set to receive calls for that phone, and 'calls on other devices' is switched off on both devices.
Being in a 'same sex' marriage, we share probably 80+% of the same contacts so sharing an Apple ID works perfectly for this. Also, just stupid things like syncing a shopping list via the "app for that" so that whichever of us goes to the supermarket has a synced list of things we need.
Thankfully, we trust each other way more than enough that this won't be an issue but nevertheless it's something you 'should' be able to configure; after all, recent calls on my phone won't be relevant as 'recent calls' to my better half.
If anyone finds a solution ....