A bullet moving with high velocity has a large momentum. When it strikes the window pane, the velocity decreases and momentum reduces to a very small value. This sudden change in momentum exerts a large impulsive force enough to pierce through the window pane, making a hole. On the other hand, the velocity of a pebble thrown at it is not very high, its momentum is less. So. change in momentum (or force) is less which only make cracks in the window pane.
