What if the MLB decided that you could use your manager challenge on an out pitch? In other words if it's the 9th inning bases loaded and a 3-2 pitch, you could challenge that if you still have one to go to the pitch f/x result.
Regardless, I have more of a problem with guys getting called out from 1st base/3rd base umps on check swings more than any plate ump calling. I swear, they just guess based on reaction from catcher/batter and get it right 50% of the time.