Its the way the weapons are set up. The damage is immediately registered but the weapon effect can (like with missiles) keep going long after the damage is done.

Damage is applied immediately once the weapon is fired (all buffs/debuffs taken into account as well). Doesn't matter the weapon type Missile, Projectile, Beam. It is the weapon effect that is still going long after the damage has already been applied. That is why it is not good to have a very long weapon effect. Try increasing the speeds of your missiles, or shortening the time of your effect.