During the close-up shots of the scene where Madmartigan and the soldier are being dragged behind the wagon, Val Kilmer was kneeling on a pedestal behind the wagon, while his stunt double was dragged behind letting the stunt man's legs take the beating.
Just after Willow's wagon goes over the fallen tree during the cart chase, one of the horses steps on the tree and leaving an imprint showing that it is made of foam.