In order to log email replies from the contacts, there are certain criteria. Could you please read through this knowledge base article(Log email replies in the CRM) and check if the email in question meets the written criteria?
If it does and still the email is not logged, please provide more details such as:
URL link to the contact record in question
A screenshot of the email you received at your inbox which is currently not logged in the contact record (Please hide any personal information such as your contact's email address. I'd want to see the date & time.)