When emails don't get saved into the expected mailbox, it's highly likely that the problem lies with the configuration of the mailbox behaviours.

To double-check:

Open Mail
Click on the 'Mail' menu then 'Preferences'
Select the 'Accounts' tab
Select the problematic mail account
Visit the 'Mailbox Behaviours' tab

If there's a problem, then one or more of the fields will be empty, meaning that Mail doesn't know where to save emails.

Resolving the situation could be as simple as selecting the right mailbox from the dropdown list but in some cases, the root cause lies elsewhere.

To dig deeper, click on 'Server Settings' then on 'Advanced IMAP Settings'.

The IMAP Path Prefix should be either blank (nothing written there) or INBOX (all uppercase).

If it's something else, then first try leaving it blank, quit Mail, reopen Mail then check the "Mailbox Behaviours" tab.

If you still can't associate the right mailbox folders, then change the IMAP Path Prefix to INBOX, quit Mail, reopen it then check again the 'Mailbox Behaviours' tab.

Even if all looks good, it's best to send and receive one or more test emails to confirm that the problem has been resolved.

And you, how often do you have issues with the Mail app on your Mac?

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