There are two issues that are major bugs dealing with custom conferences that I've seen.
The game allows you to move all teams from independent status to other conferences. However, when you do this, you can no longer make teams independent and it glitches out the conference menu so the conference you are selecting on the menu across the top is not the conference you see when selecting teams.
There is also an issue where in my fourth year I was fired from Memphis and took a job at Colorado State. I had moved Colorado State into the American conference, but when further adjusting conferences, Colorado State did not appear in ANY conference, and teams could no longer be moved. The game eventually crashed and when I tried to re-load my save, it would crash the game.
