If you have CUIC, there is a report under the traditional section (at least the report exists in 9.0x, peragt20_Agent Real Time Report) that will show agents logged in and the extension number being used. I don't know if there reports elsewhere that show the extension being used. If this report is available to you, it should show to what extension the agent is currently logged in.
I get a number of these types of trouble tickets a week because agents move around from desk to desk and don't bother checking the values in the login box to validate they're entering the correct information. I can run that report and tell the agent the extension number being used. The agent usually says that he/she sat at that extension a day or 2 before. I know this is the case when I get a ticket from each of the 2 agents kicking each other out of CAD.
Bill