I don't know if it might be lag or some other factor, but many times I find when I have my weapons set to autofire, every now and then they tend to snag up and none of them fire. I'm not changing targets or anything that would cancel AF either.
My escort for example, has 3 borg AP turrets on it's aft weapons. I set all three of them to AF so I can get a steady stream of DPS from them when I begin attacking my target. But sometimes they stop firing, and I have to click on one (or sometimes all three) turrets to tell them to fire again.
Rarely do I ever experience lag spikes in this game. Most of the times when I do, it's on the server's side, and visual latency isn't an issue with my computer's specs. This one is strange though. Heck, sometimes it happens for my KDF cruiser, which pretty much has everything set to autofire.