SIX YEARS LATER
I have an answer for you!
Unit shadows are drawn onto an invisible mesh on the ground which you cannot see the grid of
When shadows stick up wildly like that, it is because they are reacting to an invisible water layer (there doesn't have to be any water for this to happen, it's just the ghost in the World Editor)
To fix this, copy and paste tiles which have their shadows behaving onto the misbehaving patch of tiles (raise/lower accordingly) and this should stop happening.