I was having this exact same problem
I looked into the code and compared the guns that didn't work to the ones that did, and it seems that all the weapons that functioned properly spawned the projectile from within its own code, where all the weapons that didn't (Ardent, Thunder, Psy, and some others) called upon a script to spawn them, which always fails. The error message I get in game is "Cannot apply with() to undefined"
Unfortunately since my knowledge of GML is limited, I don't have a manual fix for this other than editing the weapons to fire their projectile from within it's own code. Best thing we can do is report the bug to the developer and wait for a fix.