As the title says. When auto-attack is enabled, when a big fleet is auto-attacking a bunch of enemy units, it understands that one ship has a limited amount of HP and stops firing 2 or 3 seconds or so before the ship explodes to move on to the next auto-attack target (hold Alt down). However, if you manually tell a lot of ships to fire at a single enemy unit, the ships all keep firing until the ship explodes. When you have fleets of 70 or more frigates, those 3 seconds can equate to a very significant amount of damage - it takes a few seconds for the game to update the hull/shield points. The ships on auto-attack understand this, but the ships on manual attack don't.
(Related: Rarely, when the fleet is in auto-attack mode, the targeted ship is regenerating quickly, and the fleet fails to kill the first targeted ship before moving on to the next, leaving the 1st ship with 1 to 50 hull points left.)
For this reason I don't like to order each group of my fleet to target specific enemy ships unless it's essential (eg.: capital ships, subverters, re-prioritize if fleet is targeting flak...).
I'm not sure if I would classify this as a bug, but it is a slight inconsistency which can get annoying if I feel like I should be MMing attack orders in the battle, which I would do if it didn't result in this sort of problem.