Hi@Athira Chandran,
For your question, in my experience, it may be because the email was automatically marked as spam and redirected. Sometimes legitimate emails are marked as spam by the system. If the email is detected as spam, it will not show up in the regular inbox, but may be included in the spam data reported in real time.
I'd like to ask if you know if the content of the email contains any of the typical characteristics that are considered spam - such as certain keywords, phrases, or patterns. I would suggest that you can use the Message tracking log to find more detailed information about that email. You can use this format command by the Exchange Management Shell to get:
Get-MessageTrackingLog <SearchFilters> | <Format-Table | Format-List> [<FieldNames>] [<OutputFileOptions>]