Have you tried testing this yourself by creating a new account, then another with the same email address? Sometimes people put special characters in a field when they are typing, such as a space, that may not be visible when you simply compare the two email fields.
If I had to guess, they probably didn't get their registration email from the first registration because the email address has a space or special/hidden character in it, so they registered again, getting it right the 2nd time.
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