GTFS shapes are a geographic representation of the paths traveled by vehicles in the transit system. The GTFS trips.txt file can contain a shape_id field, which indicates the shape associated with each trip. If the shapes.txt file contains shape_id values that are not used by any trip in the trips.txt file, these shapes represent paths that are never actually used by any vehicle. This is probably an indication that the shapes.txt file has an error or is outdated. The shapes displayed in the map may not truly represent the locations of the transit agency's routes.
Update the shapes.txt file to remove unused shapes.