Generally, you'd use separate trips.
For example, if the two stop-times both belonged to the same trip AND had the same stop_sequence values, it'd typically be considered a validation error, since stop_sequence should be unique for each stop-time in the same trip.
Just to be clear, there is nothing wrong with having the same stop appear in the same trip more than once, especially for loop routes. However, if aren't modeling a loop route, you should use separate trips. Otherwise, you are saying that a rider can get on at the first stop-time and ride through all the intermediate stop-times and arrive at the same stop again two hours later. Maybe that's your case, but I'm guessing not.