I've been trying to make a large double-barrel rapid-fire-missile turret (50 blocks in length 5x5x15 bricks of modules.) I've tested missile-beam, missile-pulse, missile-cannon, and it affected the 3.
This is while the turret is under AI control. A player using the cannon results in the turret firing normally.
What's happening is that the turret is firing at a 30-90 degree angle (it varies depending on the design) off from the point of fire, usually downwards from the barrel. Regardless of how the turret is designed, even when I just did the modules with the computers and ship core and bobby AI in front with nothing blocking it, no armor, no fancy designs, just bricks of modules with the computer stuff in the middle between the two barrels.
The issue is not present on other turret types (cannon or laser), only the missile with whatever secondary/effect.