quick contact showing two duplicate mobile numbers

Many of my contacts contain just one phone number, their mobile. Then WhatsApp identifies them and adds its own contact. These two contacts are merged and when viewing the contact I see only one number, as expected. However, apparently internally the G3 lists the contact as having 2 duplicate numbers. This confuses apps that try to automatically choose a default number to call (specifically, Conigri contacts widget). I can also see this in the quick contact popup. The contact shows with two entries of the same number. I can't work around this by choosing one of these as the default, because the contact details show just a single number. I tried to remove the number, which initially works as the WhatsApp number becomes the default, but then WhatsApp syncs, sees the contact no longer has a number and deletes its contact entry leaving me with a contact with no number.

Note that I previously had a Galaxy S5 and had no such problem there (so it is not a basic Android problem I guess).

I tried googling for the issue, but couldn't find it. How can I solve this?