Hi @rpodric , thanks for posting in our Q&A forum.
It seems to be backend issue, but it is suggested that you can follow the below troubleshooting steps:
- Check the user's other folders, including Deleted Items and Junk Email. It might be best to do a search through the entire Inbox and all subfolders.
- Also, check the "Recover Deleted Items" option in the Deleted Items folder.
- Check the quarantine (O365 Security & Compliance --> Threat management --> Review) to confirm that there are new messages for which notifications should be sent.
- Please run the message trace and check whether there are any quarantine notifications were sent to your account.
- Temporarily disable any additional spam filter policies you may have configured (O365 Security & Compliance --> Threat management --> Policy --> Anti-spam settings).
- Temporarily disable the End-user spam notifications. Leave this disabled for a few hours before reenabling it.
And I have found a similar post here for your reference: https://answers.microsoft.com/en-us/msoffice/forum/all/not-receiving-o365-quarantine-notification/535a2eab-20ac-4b65-abe7-a77ff8a3b6fa If there are any update, please feel free to let us know.
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