Although I kind of expect this to go unread by the other poster...
Short version: Pause and switch teams when you see a high foul ball heading into the field box seats on either side of the foul lines. The bug will not trigger when the fielder is user-controlled.
The bug does not happen on every foul ball (or even close to it), it takes a specific location and height to allow the fielder to run into the wall and fool the boundary. I probably don't average one of these per game, though it can happen 2 or 3 times in a game. Just depends on how many foul balls you hit. It's annoying, but not horribly immersion-breaking to switch teams when I see this coming.
Unfortunately, there is no fix for this in RTTS.