When you are trying to blow up walls with your Yellow Pikmin and have bombs remaining after the task is completed, keep them. They are very useful for killing enemies. Keep the Pikmin with the bombs away from the group. If a bomb explodes, your entire group may die. To use the Pikmin with the leftover bombs, simply throw them at the target and call them back. This will either injure or kill the enemy. If the enemy is not dead just call your group and finish it off.