There is a way to sort this out.
Obviously, your wife has two separate Mobile/Cell phone numbers.
On each phone, ask her to go into Settings > Messages.
iMessage should be "On" on both.
Under "Send & Receive", Select, by tapping, the number associated with that phone only and uncheck any other numbers. You will check the iCloud.com associated with her Apple ID on both.
"Start New Conversation From" should only have the number associated with that phone only. I don't have any iCloud.com checked on either in this section.
In other words, your wife's situation is no different from my wife and me, as we both share my Apple ID. I understand from these forums, that many couples do the same.
With the settings I've mentioned, neither my wife nor I get any messages meant for the other.
Please let us know if this works. Any problems, I have another possible setting change, but that shouldn't be necessary.
Ian
