The stop_lat and stop_lon fields in the GTFS stops.txt file define the latitude and longitude of stops. These fields are permitted by the specification to be null if the stop's location_type field has a value of 3 or 4. However, because this tool creates geographical features to represent stops, it cannot map stops that have no latitude or longitude. Consequently, stops with location_type values of 3 or 4 that have null values for stop_lat or stop_lon are skipped and are not included in the tool's output.
As long as your input GTFS data is correct, you do not need to take any further steps.