If a user is seeing the warning "Email has already been taken," this means they already have an account, whether they realize it or not.
If a user is not aware they already have an account with you, it usually means they started the checkout process but never made a purchase, or that they previously signed up for free access or content. In either case, this means they never made a payment to your store. However, it's also possible that they have already made a payment and simply forgot they had an account.
As an admin, you can reset their password for them by following the instructions, here. Or, you can give them the instructions in this guide so that they may reset their password themselves.
As an admin, you can reset their password for them or send them instructions on how to reset their own password. Bu following those steps, the user will regain access to their account.