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In Batman Begins, Bruce Wayne is shown to have fallen into a well and had his first encounter with bats when his Father was alive who then ropes down the well to rescue him.
Whereas, in Batman vs Superman, Bruce is seen to fall into the well after his parents' demise.
Is this an intentional discrepancy and one that was introduced to separate this story from the previous Batman trilogy?
Batman vs. Superman is in continuity with Man of Steel, but shares zero continuity with Nolan's trilogy, also referred to as The Dark Knight Trilogy. This new series of films will be referred to as the DC Extended Universe.
As such, the writers are able to take liberties with various portrayals of events in the mythos of Batman, including how he developed his fear of bats and his resulting decision to use them as his symbol for justice.
In Batman vs Superman the fall into the well is, at least somewhat, part of a dream sequence "in the the dream the bats carry me to the light." It does part from the Nolan trilogy in many ways. This one seems like a minor one.
