I don't mean to be funny here, but the answer is 'sometimes'.
MLB instituted the use of instant replay during the 2008 season. It can be used to determine whether a ball left the park for a home run and to determine whether there was fan interference on a play. But unlike the NFL, where the coach has a red flag that he throws onto the field to indicate a challenge and instant replay will be used to determine the correct call, the MLB manager has no such ability. All 'challenges' are initiated by the crew chief of the umpires working the game. So it might be possible for the manager to convince the crew chief that the play was called wrongly and have instant replay used. But if the crew chief believes the call was made correctly, and usually he consults with the other umpires to get their interpretation of the play, there is no chance that instant replay can be used.
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