Disadvantage can be called for by the DM in any situation where she believes the situation warrant's it. I would say shooting into a melee scrum is a good example of this, but should be ruled consistently by the DM. IE maybe DM decides the shot is at disadvantage anytime the attacker is more than 1/2 the close range of the attack or if there are more than 2 of your allies engaged.
For that matter, you could also say that 2 allies engaged with an enemy you are attacking counts as 1/2 cover, 3 is 3/4 cover, and 4 is full cover (adust for enemies larger or smaller than enemies engaged).