Very likely that Contacts in the Cloud came over. Possibilities...
- Contacts saved to the phone/sim did not come over.
- Contacts associated with multiple ‘accounts’ and not all accounts loaded with Contacts synced.
My $0.02:
Find the best ‘list’ of all of your contacts, export to a .csv file and then import into your MAIN email account. Clean up as needed and then only sync Contacts from THAT email account. Make sure in Settings - Contacts that the correct email is assigned. I think it will be automatically if you only sync Contacts from a single account.
I have 1 Yahoo account, 1 iCloud and 2 Gmail. I sync Contacts from just one of the Gmail accounts. The rest just bring in email.