This happened to me the first time I tried to put a Gauss Cannon onto a Mudskipper Mk.2. The ship would dance about and not fire, until its Simulation enemy eventually sprayed it down.
... A couple of days later I tried again and the issue did not repeat itself.
So, yes, I can confirm this happens sometimes in 0.95.1a , but sadly I have no further information on how. It is certainly not reproducible on demand.
[...] Part way through the fight, I'd settled down into a close broadside to the station, having killed off all the ships nearby and one of the three station sections, and was pouring fire into a second section - only, the Storm Needlers (and possibly other guns, but the Needlers were really easy to notice) weren't willing to fire at that section, despite being easily in range and having an empty flux bar.
[...]
I think this might be something different. I have an Onslaught build with Heavy Mortars in the three front-most medium slots and those almost never fire at station segments. Not only are those not kinetic, it is also a much more frequent occasion (not-quite-reliably but more reproducible than not).
... Maybe try and check (or remember) whether your ship had an explicit attack order against the station? That seems to much exacerbate this issue for me (to other/more weapon slots; not 100% sure though) - I think the ship tries to aim weapons at the segment on the far side and registers the rest of the station as blocking their line of fire.
So far I have not been sure enough about what I am seeing here, so I have not yet reported it, but what you describe sounds like more of the same, so if you could confirm or deny... ?