Automated Over-Quota Message:

Why do I get "over-quota" messages when my INBOX is empty?

Unfortunately the Exchange Mail Service Web Interface (also known as OWA) has several built-in automatic features which can cause messages to build up without your knowledge. 

First a copy of ALL messages that you SEND are automatically saved within the SENT ITEMS folder by default.

Second, any items you delete from a folder (like INBOX or SENT ITEMS) are sent to the DELETED ITEMS folder but are NOT automatically removed from that folder.  Thus all message items really take TWO deletes to remove. Your first delete moves the item to the deleted items folder, then you must EMPTY the deleted items folder to completely remove the item from your mailbox. 

Remember that using theSAVE button within the NEW message window, will save a copy of the current UN-SENT message into the DRAFTS folder.  This message should either be sent at a later time or removed manually from that folder if you are not going to send it.

If you don't explicitly manage [empty] your DELETED, DRAFTS and SENT ITEMS folders as you work; you will eventually run out of space.