This indicates a problem in the GTFS dataset. The service_id field in the trips.txt file should refer to values in either the calendar.txt or calendar_dates.txt file, or both. These files define the dates or weekdays when the transit service runs. However, neither of these files contains the service_id field found in the trips.txt file, so the dates or weekdays that the trip runs are undefined. The tool will not fail in this circumstance, but the output Runs table may be missing some transit service.
Add the missing service_id field value to the calendar.txt or calendar_dates.txt file, remove the references to this service_id field value from the trips.txt file, or ignore the warning.