When upgrade a mod, if files have been renamed or deleted, then the old version of the file is not removed.
When the code in ModManager/ModSystem/ModExtractor.cs was changed to support update 6 the folder name was changed as such:
-var modFolderName = $"{modInfo.NameId}_{modInfo.Id}_{modInfo.Modfile.Version}";
+var modFolderName = $"{modInfo.NameId}_{modInfo.Id}";
but ClearOldModFiles only works if modFolderName is different, so without the mod version suffix it won't remove old files.
ref: https://github.com/TobbyTheBobby/ModManager/commit/6dc62d16e4de214bd4971feb34384c08e51cf8e9#diff-41f14a3c19303c9a2648518d483e19c1d9d0e259678e2df4340c7e62c08d621dR24