Many years ago, flying in coach, AA split a thru-flight into two segments and assigned me different seats for each segment since there was no seat available for the thru-flight. I was issued two boarding passes. Naturally, I stayed on the plane when it stopped. So, the second boarding pass was never scanned. The gate agent came on the plane before we departed to verify that I was on board. Later, I had to have the mileage manually credited to my account.

Another time I submitted an upgrade request for a thru-flight ahead of time. It didn't go through. I was able to get a gate agent to manually add me to the upgrade request lists for the separate segments. They didn't go through. I might've had better luck had I called AA ahead of time to be added to the lists for the separate segments.