I have the Emil fleetstar mod installed and all upgrades are a buck. This effects the upgrades on the normal fleetstar as well they are all also a buck. And some of the upgrades like engine are available on the normal fleetstar too! This problem is present on other trucks too where modded truck upgrades affect normal truck upgrades.

Thats because they don't change the file names(engines, etc.) that they edit and update the xml for the new file name.. its not a bug.

You should put that on mod io under the comment section of that particular mod who probably work the way you are facing right now, if not at least the creator could look into his work to validate weither or not it is intended.