I was just testing myself and I'm not able to recreate what you're describing. I equipped 3 missile weapons and 1 ballistic and they were firing fine. The only thing I can think of that could have caused this is an incoming damage feature that is implemented to prevent all weapons firing at the same target if its not needed. So this means that it can sometimes seem that the shorter range weapons arent firing at an enemy if a missile is already headed for that enemy. This was implemented to make for example multiple missile launchers viable option so they wouldnt all shoot at the first target they can and get hit by other enmies while reloading, instead they fire at one enemy each. Maybe this feature should be emphasized or explaiend better somehow.
If what I described isnt what youre experience it would be greatly appreciated if you could just briefly describe your weapons setup (with upgrades) and speed your playing on when experiencing this issue so I can try recreate it.
Thanks again for the feedback and sorry for the bother.