This doesn't change your complaint - a long season hurt by a computer problem at the end, but here's what probably happened.
When you submitted your lineup, you probably hit the submit button twice. I've done that, I hit it once and it looked like nothing happened, so after 10 seconds or so, I hit it again. I've done that for a home game and my players came out all scrambled exactly as you said. I'll bet it happens in away games too.