MC does not rename "fanart.jpg" files, When scraping, MC looks for existing fanart in all naming conventions, if such a file exists then it will not download a fanart.
It sounds to me like you have all your movies sharing a folder, yet "fanart.jpg" is a valid naming convention, often used when people have each movie in its own folder. since you already have fanart.jpg in the same folder as each movie then MC believes that the movie already has a fanart.
The same is happening when browsing, MC is checking all naming conventions for the selected movie that exist in the same folder and finding "fanart.jpg"
This is not a bug, it is the intended behaviour that allows media companion to support all naming conventions.
What might be a bug is why the "fanart.jpg" is created in the first place
Ensure that the option (Save files as "movie.nfo", "movie.tbn", & "fanart.jpg") Is not checked in the preferences.
If you can reproduce fanart.jpg being created then please let me know.
Other than that, as you said, now that the fanart has been deleted then the issue should be permenantly fixed.