I've played through almost 3 full seasons of rising star, and have a pretty good method of avoiding this bug. I'm playing on Xbox One, it may or may not work for you on other platforms.
The bug usually happen when you skip a cutscene while the ball is loose on the ground. When you skip the cutscene, it jumps to the point where the ref is supposed to pass the ball to the free throw shooter, but he doesn't have the ball because the ball never got picked up (because you skipped ahead). In some camera angles you can see the ball sitting on the ground.
So to avoid this: DONT PRESS ANY BUTTONS TO SKIP AHEAD AFTER A FOUL UNLESS THE REF OR THE SHOOTER IS HOLDING THE BALL. Wait until the ref is holding the ball, then press a button to skip ahead. Then wait until the shooter is passed the ball before skipping again.
This isn't perfect - I had a recent game where the shooter bricked the shot badly and it rolled out to the 3 point line where the ref wouldn't go get it, but I'd guess I'm down to maybe having to restart one game out of every 20 or so.
Hope this trick helps somebody else out.