Missle units usually do not follow orders to target enemy units in the second line when there is another unit between them and the target. They will shoot on that unit instead. Sollution: none, that I know of.

Another problem are units in formation: when you order the entire formation to attack a specific enemy unit and there are other enemy units closer to some of the units in your formation they will attack those instead. Sollution: give the order to every single unit in your formation.

On the slingers: Units in larger formation, espacially if these happen to be in wide order, might 'crash' with enemy units when ordered to manouver close to the enemy. Even skirmish mode won't prevent a melee in this case. Sollution: Move them like ships. Give them a destination far from the enemy formation, and once the got 'clear' the enemy, move them in again.