Check the notification's settings
First, make sure that the notification has been correctly set up:
Go to Setup and click Settings.
Click Notifications.
Click the notification in question.
Click Edit in the Emails area.
If this needs to go out to the employee's line manager, the recipient needs to be set to Reports To.
Click Save.
Check the employee's line manager
Next, make sure the employee's line manager has been set up correctly:
Search for the employee and go to their profile.
Click Employment, then Position.
Click Post Details.
Click Approvals, then Approver.
Click Edit in the Reports To area at the top of the page.
Select the post that needs to be the line manager.
Click Save.
All future notifications will go to the correct email address now, but this will not impact emails that have already been sent.