I think if your system supports both social media and email logins then you should allow both to be linked to the same account.
So the next time a user that has signed up through social login tries logging in through email, you can redirect him to sign-up screen saying that "there is no account with the given email id. Please try logging in via social login in case you created an account with that" (Do not mention if that user id already exists through social login since it is considered as a privacy/security breach -- some crawler can know which user's have signed up for your service and attack them via phishing).
This way, the user can still signup via email with a password and you can connect this to the social login usage, thereby allowing him to login via both options next time. If user logs in via email first and then tries to login via social login then its way simpler since you just need to allow him to do that.