In Plato when replacing a selected station on the sheet (click the graphic file, right-click and choose replace station), you replace just the selected occurrence of the station by a new one, i.e. the original station remains in the station list, and a new one is added. This means that the inks used by the old one can't be cleaned up (as there is still a station in the list using these inks even if there are no instances of this station placed on the sheet). When you use 'assign' instead of 'replace' or when you replace that graphic in the station itself, then the old graphic no longer exists and it's inks can be cleaned.
Open an existing Plato file. Right-click the station file and choose Replace. The file replaced had different inks and hence these inks are just added to the list. The inks from the original station are not being removed.
Open the file in Plato.
Click the Stations link at the top bar. The Stations window will open.
Right-click the station file you wish to replace. Choose Replace station.
Browse to the file that is replacing and click Open.