At our company, this tends to come from either Outlook moving emails to spam/junk by some logic I will likely never understand, or that the corporate level is filtering (in our case, multiple levels of filters) and catching some Workfront emails. Some of them make it into periodic quarantine emails from Microsoft, some don't. It is often very user specific.
What also happens is WF will update it's "you need to whitelist all these dozens of domains, IPs, etc." without notification. I find out beause suddenly people don't get notifications, I then scrape the whitelist info from WF, then our Messaging group updates things, and all is well until next time.
One exercise WF should be able to help you with is to provide the unique message ID for any email notifications they say went out but you did not receive. Then your own IT/Messaging group should be able to trace if it got blocked at their end. Tedious, but helps with troubleshooting.