Maybe it's because you are keeping the contacts on the device, not in the GOOGLE account. On the agenda, configuration, there is an option that says contacts to display. There you got to select the account contacts GOOGLE, I mean the account you set up your phone.
But you appear you got to keep them forever in that account and not on the device.
To fix now export all contacts from the device to the gmail account.
And every time you save a new contact and notice that this placed the option GOOGLE account.