There is a string on support.zendesk.com where a Zendesk Administrator is asking how to differentiate between tickets created by customers and tickets created by Zendesk Agents.
By design, Zendesk categorizes Agent-created tickets and Customer-created tickets from your Help Center (Guide) Website the exact same way: via Web Channel.
For me, I discovered this thousands of tickets in to a Zendesk setup. I hope you got here sooner than I did!
Here's how I worked around it:
I created a trigger that adds a tag (I used agent_created) when an agent is submitting the ticket via the web (aka normal agent behavior). The trigger fires when:
the ticket is created,
AND current user is an agent,
AND Channel is Web form.
Remember, triggers are NOT retroactive. Meaning, once you put one in place, they will fire on any tickets it applies to that are in <Solved status, NOT Closed status. Why? Closed Zendesk tickets are not editable. Therefore, when running reports, keep in mind the date you put this trigger into effect and factor that in. Don't worry, before you know it, you will have Good Data again. (See what I did there? Clever, I know.)