From your description, it sounds like the Contacts app on your phone now has content in it from two partially merged Google accounts. Something to keep in mind is when you've set up your phone to sync with your Google account, it's your online Google account that's the primary and your phone is simply the secondary. It's your online Google account data that resides in Google's servers, and then when you use your phone or when you use a web browser on a desktop computer all your doing is remotely accessing that online data. On occasion, like when your phone doesn't have online access (you're disable WiFi and mobile data), some data will just be held on your phone but once it has online connectivity again it's just merged with your primary Google account.
So with the Contacts app on your phone apparently holding contact entries from different Google accounts, what you need to do is reset the Contacts app to its original state on your phone; and then clean up the contact entries in your Google accounts using a either a web browser on a computer or your phone. And you need to do this while Contact syncing is disabled so once everything is straightened out, you enable syncing again so the online Google account data just repopulates the Contacts app with the now cleaned up Contacts data.
-- Open up the Contacts app on your phone, make note of any contact info that's only on your phone and not in your Contacts when you access your Google account using its web interface (using a web browser on a computer or on your phone.)
-- Now go into your phone's Settings >> Accounts >> Google menu and disable Contacts from syncing.
-- While still in your Settings menu, go to Apps, find and open the Contacts app entry, tap on the 'Force stop' button and then find and tap on the Clear data button. Using Clear data wipes the app's settings and config data, along with the app's cache. This essentially returns the app to its original, unused status.
-- The next step is to clean up the Contacts in your online Google accounts. Use a web browser on a desktop or your phone (a desktop/laptop will have a bigger display and make things easier) and go to
http://contacts.google.com. Log into your respective accounts and clear out any duplicates, add in missing entries, etc. Get both accounts cleaned up and organized. In the left side column there's an Export menu where you can save your Contacts list as csv or vcard file as a backup just in case something goes wrong.
-- With the Contacts data in your online Google accounts cleaned up, now go back to your phone. Go into Settings >> Accounts >> Google again, enable syncing with Contacts again. Depending on how many contacts you have, it may take a few minutes to repopulate the Contacts app with your data.
At this point the Contacts app should be showing just that one Google account you've chosen. Do a quick test by creating a test entry in your Contacts app on your phone to see if it then shows up in your online Google account. Do the same in the web interface so that test entry hen shows up on your phone.