Hi Duncan,
To narrow down the issue, I want to confirm some information first:
1. Did the issue occur on Outlook Client or Outlook Web App, or both?
2. The sender is in your organization or out of your organization.
3. Did the delayed emails come from the certain sender?
In addition, here are two suggestions for your reference:
1. Refer to Inbound mail flow to check if Office 365 have received the email on time.
2. Check the Service Health and Maintenance section in Office 365 portal, if there is some related information about this issue.
Thanks,
Eben Liu