Well, first of all, you cannot have friendly fire casualties caused by missiles from the same unit. Also, whenever throwing javelins/pila remember that the closer the better. My personal favourite is to let an enemy unit engage mine and then send another javelin-throwing unit behind the engaged enemy, as close as possible to that enemy unit as one can get without actually going into hand-to-hand combat. Then I will order that javelin unit to fire. Usually the casualties from the first volley are at about 40-60% for a 25 defence unit. After the second volley that enemy unit is routing. All that from a unit whose javelin attack is 6.

Oh, and keep in mind that as MAA said, if your unit is already fighting, ordering them to fire at the enemy is a huge blunder. Especially if you are fighting cavalry, who has a large push value. Not only this, but very few javelins will actually be thrown.