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iPhone has probably one of the better hardware devices out there.
iPhone has probably one of the worst software out there.
iOS will try to sync your contacts with your email accounts and will just do anything without notifying you in the worst way. I found the easiest and most beneficial way to fix this (for me) was to actually take time to clean up my email contacts. Then best to remove the account from iOS and re-add it again to make sure.
clean up means, last name, first name, email and phone number at the least.
Since then I have had little issues. (iOS is capable of switching things on and off just for fun, so even if you would not allow syncing contacts, sooner or later, somehow, it will)
The iOS Contacts app creates a "Group" for each e-mail account. These groups can be turned on/off within the app. There is even a "Hide All Contacts" button to turn all the groups off. I'd start there.
Also, within the main "Settings" app there is a category for "Contacts" that allows you to set the default account for when a contact is created on the phone. This can be overwritten during creation by turning off all the groups except the one where you want the contact to be created.