Every once in while, the AI manager does something really stupid, sometimes in a pennant race or maybe in a playoff.
Every once in while, a real MLB manager does something really stupid, sometimes in a pennant race (see 1964 Phillies) or maybe in a playoff (see 1986 Red Sox, World Series, Game 6, etc.)
Every once in while, the AI GM does something really stupid, usually along the lines of a dumb trade.
Every once in while, a real life GM does something really stupid, usually along the lines of a dumb trade (see November 29, 1971 - Astros trade Joe Morgan and others to Cincinnati for Lee May and Tommy Helms, etc.).
So, when the AI does something really stupid, I just smile and call it the John MacNamara factor.
Just think of it as extra added realism. It the AI manager/GM did the right thing all the time then you wouldn't be simulating real baseball very well, now would you?