Hi there,
To clarify, are they logged in as you mentioned, or just have existing accounts and are trying to Check out? Are you able to reproduce it on the site as well while logged into your account?
This message can be displayed if they have created an account, and are trying to enter their email at checkout in the email address field but have the “Create account” checkbox checked as well (while not actually logged into their existing account).
We have also seen cases of this being incorrectly displayed due to conflicts with other plugins or themes that include login-related functionality as well. To check for conflicts, please temporarily switch your theme back to Storefront and disable all plugins except for WooCommerce, then check to see if the issue is fixed. If it is, then you can switch your theme back and reactivate plugins one-by-one until you find the one that is causing the issue.
You can read about testing for conflicts in our documentation here:
https://docs.woocommerce.com/document/how-to-test-for-conflicts/
If you are still having trouble, please share a copy of your site’s System Status. You can find it via WooCommerce > Status. Select “Get system report” and then “Copy for support”. Once you’ve done that, you can paste it here in your reply. Please note that since this is a public forum, you may want to remove any sensitive information that you don’t want shared publicly.
Also, send screenshot of the settings under WooCommerce > Settings > Accounts & Privacy. I recommend https://snipboard.io for easily sharing screenshots – please follow the instructions on the page, then paste the URL in your reply here.
I hope that helps!