Secondary gun on multiple ship have issue with their shell landing 250m further than where you are shooting with your main gun.
For example, when i am firing at a target 10km away my main gun shell will land directly on the ship but the secondary shell will always fail to hit the ship because it land at 10.25km.
I might be wrong but i think the issue is the shell speed difference the automatic calcul in the game might not take that variable in the equation. Same gun elevation for different shell speed will make main and secondary gun shell land differently.