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 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 This is probably an indication that the shapes.txt file has an error or is outdated.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 accurately represent the locations of the transit agency's routes.
Remove the rows referencing the unused shapes from the shapes.txt file or, after the tool finishes running, delete the features from the output feature class that have these shape_id values.