The plugin’s login function is simply a wrapper for wp_signon(), which is a core WP function. WP logs in the user with wp_signon, and the user’s login state is checked with the WP function is_user_logged_in(). So whatever the issue is, it’s unlikely to be in the plugin.
WP (and thus, the plugin also) allows a user to log in with their username OR email address. BUT… that’s not to be confused with the email address being their login. WP requires a user to have both a unique username (user_login) and unique email (user_email).
The only thing I can think of is if you have applied some kind of customization to register users with their email address as their actual username without accounting for users changing their email address. WP doesn’t allow for usernames to be changed, so if a setup was customized to apply the user’s email address into the user_login field and a user changed their email address, they could potentially have a mismatched login.
To track down your issue, you’d need some insight into what users this has happened to, what their user data is, and look for anomalies that might lead to some clues.
