No idea why this is happening but I have the same problem. If I can't fix it until the next update I might just remove the sound.
I think I found the problem. The ranged attack animation and the factory animation are fighting, as a result the structure thinks it's always starting a ranged attack, and so launches an arrow. I'm not sure if there's a way to fix that with the mod, outside of removing the transformation or removing the ranged attack.
The animation logic is different in 2.2, so it shouldn't be a problem then.