Messenger continuously syncs contacts from your phone. If you want, you can turn syncing off.
Anyway, you can remove your non-Facebook friend contacts very easily. Follow these steps:
- Tap People
- Tap Info against the person you want to remove
- Now Remove Contact
If your synced contact list is too long to manage, you can remove them altogether from Facebook.
Try following these steps:
- Go to https://www.facebook.com/mobile/messenger/contacts
- Now Delete All