Why a POP client (such as Outlook) automatically moves emails to Trash folder.

Yahoo! Mail moves messages that have been deleted by a POP client to the Trash folder, rather than deleting them immediately from the server. This means that every time you access your account with an email client (Outlook, Windows Live Mail, Mac Mail, Thunderbird, etc.), the client will copy the messages to your computer and those messages will go to the Trash folder in your Web-based Yahoo! mailbox. This will allow you to recover messages that have been accidentally deleted by your POP client.
 
Unfortunately, this feature cannot be modified or disabled.

To completely delete the messages, you will need to access the Trash folder and delete the message from the Trash or wait until they are automatically deleted.

Note: If you did not intend to have the external client perform this action at all, and prefer to keep a copy on both the client and in your online Yahoo! Mail account, consult the manufacturer of your mail client for assistance configuring your device settings to prevent this from recurring.