In a case like you describe above the service member in question would probably not get into trouble. When I was in the Army I was stationed in WA. I had gone home on leave over the holidays and arrived back at SeaTac airport a couple of hours before midnight on the last day of my leave (you have to be signed back in by midnight). It was about an hours drive to the post so I was doing OK time wise. It turned out that my luggage had missed the connecting flight and the airline had to fly it in from Denver, which would take a couple more hours. I called my unit and explained what happened and they said just get back as quick as I could. I got back and signed in about 4:00 AM. All they did was charge me an extra days leave and nothing more was said.