Most of the admins are familiar with Clutter in an Office 365 mailbox these days and have mixed opinion about the feature. Machine learning is in its early stages and things can only improve.
Users will raise calls if they don't see an email they are expecting in their inbox - that is the most common behaviour. Most of the users will have a long folder structure within their mailbox and may not notice the emails in the clutter folder. Admins can tackle the problem for once and all, by removing the feature for all the mailboxes or they can selectively disable it for the non-techie / "sensitive" users ;-).
In order to disable it for a single user, run the command below after connecting to Exchange Online.
Set-Clutter -Identity user -Enable $false
Run the command below If you want clutter to be removed for all the users.
Get-Mailbox -ResultSize Unlimited | Set-Clutter -Enable $false
A user can disable the feature themselves by logging into Outlook Web App and navigating to the Mail options page. Uncheck the box within the Clutter tab and click save.
A point to note is that the clutter folder will still be visible in the mailbox even after the feature is turned off. This is by design.