Why are there duplicate contacts in WhatsApp?

This is usually because your iPhone contacts contains multiple contact "groups". This can occur if you sync your iPhone with services that support contact syncing, such iCloud, Facebook, GMail, Yahoo! or Hotmail. Check in the Contacts app for a Groups button at the top, as shown here:

The built-in phone app is able to resolve these duplicates by "linking" the duplicates together. Most third-party apps, such as WhatsApp, do not yet have the ability to use the "linked" or "unified" contact system, and as such, will show duplicates or even triplicates.

At this time, the only way to resolve the duplicates is to consolidate your contacts into one group. The ideal way is to eliminate the "On my phone" group and use only one service, such as iCloud. Please back up your iPhone to iTunes and investigate the procedure thoroughly before attempting to remove any contacts.

If you need a quick resolution, you should turn off contact syncing in iPhone Settings > Mail, Contacts, and Calendars

Learn more about resolving duplicate contact entries from this Apple Support page.

Cheers,
WhatsApp Support Team