You really think that happens in MLB on more than a very rare occasion?
I see it all the time. Announcers love to point it out and drone on about the bad baserunning. McCarver will drone on about how it is drilled in to every player. I even see it from veteran players and world series teams. All you have to do is watch a few games. Put down the strat dice, purchase some tickets, and go see the local team. If you do not live near a local team games are all over television now. I promise you will not have to watch many games before seeing a bad baserunning play.
I understand they have meetings and drills and everything else. But when they get out there actually playing split second decisions have to be made. Emotions get involved. Players are human.