When the bullet strikes the glass pane, the part of the glass pane which comes in contact with the bullet immediately shares the large velocity of the bullet and makes a hole. While the remaining part of the glass remains at rest and is therefore not smashed due to the inertia of rest.
But when a slow-moving stone strikes the same glass pane, the various parts of the glass pane gets enough time to share the velocity of the stone, and thus the glass is smashed.