I had a bad experience using the Southwest app to do online checkin yesterday. I had a flight from Amarillo to Austin with a connecting flight from Dallas (same confirmation number). When I did the online checkin, it displayed only the first leg with A41. It seemed strange not to see the second confirmation # but it clearly showed that I was going on to AUS. At Amarillo, I printed my two boarding passes and flew to Dallas. In Dallas, I glanced at the boarding pass quickly and lined up with A43. To my surprise, I discovered that I was a "gate crasher". The GA said "Sir, you are B43. Please take a nearby seat until your number is called". I was more puzzled than embarrassed. How could I have gotten such widely different boarding numbers on a connecting flight with the same PNR? I sincerely thanked the GA in Dallas (WN3487) for catching my mistake and the courtesy with which he treated me when I was so clearly in the wrong.