There could be a randomization element introduced to let certain poor baserunners go through stop signs on occasion (and maybe other especially daring players). You see athletes ignoring instruction in probably every sporting competition. The same thing happens in pro football when players decide to field punts within their 10 yard line, instead of letting them bounce and hopefully roll into the end zone.

Like (I think it was) former Pilots manager Joe Schultz said, "I managed good, but boy, did they play bad."