If you're sharing an Apple ID across multiple iPhones, you have likely ran into an issue at some point with one phone having something from the other phone. For this post we're talking specifically about missed call history.
If you have missed calls for one phone showing up on another phone, turn off iCloud Drive. You can do so by going into Settings->iCloud, then toggle the iCloud Drive setting to off. Make sure to verify it is off too. I've seen it take a couple tries to get it to actually go to off.
Once it's turned off the missed call history will no longer be getting synchronized, and won't show up on other phones signed into the same Apple ID
