They get subbed out in both A and B. I'm surprised more people don't have the problem. It's happened to me at least 5 times, though it hasn't happened recently. Maybe it does only happen in blow outs? I didn't think to make that connection before.
I always felt crazy because my trainees randomly got subbed out every other week using starter, bench, reserve, with strictly follow depth chart, and with less than 9 players dressed. A few friends didn't have the problem half as often as me and they blew teams out too. It's weird.