The MLB umpires and the mangers are not really fighting about calls. What they are really fighting about is team managers that want thier teams to be winners at any cost. This is what just about any argument in sports is all about, especially professional sports where there is a great deal of money involved.
No, they are not simply arguing about the call. A manager will often argue with an umpire out of frustration due to his team's shortcomings. Managers understand how arguing will excite their team, and by being ejected will encourage his players to win for him. Sometimes the arguments are simply to inspire morale.
Generally, if he strikes out looking the batter may question the umpire's eyesight or judgement. He may also be telling the umpire that it was a good call if he realizes it was a good call. If he strikes out swinging he may be asking the umpire whether the ball was in the strike zone.
When you see them mumble to themselves as they walk back to the dugout, they may be complaining about the call, or they may be cursing themselves out for a lousy at bat.
Most arguments are not the result of a single call, but are the culmination of a few calls. Umpires must make snap judgments hundreds of times in a full length MLB game and managers must navigate with the strategy of a military general which calls the protest and which to hold their tongues. This is a complex strategy game that the coach must use to his overall advantage.