As others have suggested, this might be a Google Contacts issue. If you have access to a computer, navigate to contacts.google.com & select 'duplicates' from the left side of the window.
I no longer have multiple contacts after the latest update to the Phone app from Google.
Today I received the version 16.0.184589931 of the phone app, but the situation remains the same, contacts with information from messaging apps, such as Whatsapp and Telegram, are displayed multiple times.
Neither the use of third-party apps, as suggested by Marius works.
Twitch! Contacts Formatter seemed to work, but at the first synchronization it returns everything as it was.
At this point I think that the Phone app has problems with the different formatting of the various contacts.