Autofiring, whether ground or space, interferes with activating other powers. A space example: I'm fighting and see that my sheilds need some regen. I hit Emergency power to Shields & keep fighting only to see my shields keep going down. I look at the power tray & yep it wasn't activated. This affects all powers.
I know this is a problem with the game engine, since CO did the same thing, but please try to fix this.
Just go to the Key options in and look for "Fire All" then assign it to the SPACE button then just spam the space button constantly in battle. That's what many of us are doing. Autofire so far just bugs you or gets you in trouble by attacking targets you don't intend to attack.