Well, there ya go... just re-run the V3 Main Installer real quick. ;)

This happens if you install V2-era DLC to V2's default location (which is perfectly fine). V3 is programmed to check for such a thing so that it can update and transfer that DLC into V3 as well.

It might tell you to use "Update and Repair" mode; don't worry about that, just run the V3 Main Installer real quick and it will update and move the files automatically without harming anything else. Originally, V3's installer was going to have such a mode selectable by the user, but turned out to be unnecessary; El Programmerdero simply forgot to remove that text from the message.