Check whether you are using filters on incoming (or outgoing) messages. These could be automatically moving your messages to another destination.
Check your search view in the search bar right above the message list. Perhaps the Show dropdown list is set to a filter like Read Messages, or the text input filed contains some value. Click the broom icon to clear the search field.
If you cannot see any emails at all in a folder, check that you have not maximized the message preview (so the message list pane is hidden). To do this, click View ▸ Preview ▸ Show Message Preview.
Look in the Junk folder. Messages that are marked as Junk disappear from the original folder and are moved to the Junk folder.
Click View ▸ Show Deleted Messages to make sure all messages are visible.
Check your default folder under Edit ▸ Preferences ▸ Email Accounts ▸ Edit ▸ Defaults. Perhaps it is set to some other folder than the folder you thought of.
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