That's not really a bug either. The factories seem to stack up just fine. The issue is because the queue is tied to the Gravity Well, and not to the frigtate factories.
When a ship is produced at a gravity well, it goes to the first available spawn point to make the ship. The spawn points become ready almost instantly, so a ship built a half a second later can pop up at the same spawn point. This gives the illusion of one factory pumping out all the ships, while the rest are doing nothing.
Try it with four factories and a starbase. That base will be pumping out ships faster than octomom, while the factories just sit around doing nothing.