This warning indicates a problem in the GTFS dataset. The stop_times.txt file refers to a stop_id field value that doesn't exist in the stops.txt file. Because the stop's location is defined in the stops.txt file, the stop_id referenced by stop_times.txt has an unknown location and cannot be used to construct a feature in the map. The LineVariantElements features connect stops to each other; however, if the stop's position is unknown, a LineVariantElements feature cannot be successfully constructed. The tool will not fail in this circumstance, but the output transit lines may be missing segments.
Add the missing stop to the stops.txt file, remove the references to this stop_id from the stop_times.txt file, or ignore the warning.