I have recently discovered an issue on why my crew would haul ammo (usually missiles) across the ship when there is a viable factory already nearby the storage and weapons. My observations have concluded that the issues lie on the priorities and misleading crew numbers.
The problem with priorities is that all crew members prefer to reload ammo than energy. Of course, reloading ammo is important because it allows you to destroy enemies, except when your factories run out of power, they would still choose to reload ammo. I had a factory on each side with storage and missile pods. Whenever one of the factories ran out of power, every reloading crew member would run across the ship to pick up ammo and run back across. This causes severe congestion problems and a vastly reduced efficiency on ammo based weapons (again, usually missiles).
The second problem is the misleading crew number requirements. Since the biggest offender currently are missiles, I will use them as an example. On a single missile pod, a full load takes 12 canisters and 2 operating crewman. Each of those canisters can only be reloaded by a single crewman, regardless of where he may be located. This is reflected on the crew requirements when you build it as it increases by 2 for the minimum and 12 for the recommended. However, storage does not change any of the requirements. If you have 1 missile pod and 2 missile storage, you actually need 36 reloaders. This issue is also linked with the previous one about priority, where your crew would prefer to reload ammo than reload energy.
Currently, the only way to bypass this is to either not have ammo storage or have minimal amounts. However, one small change could easily fix these issues. Crewmen hauling ammo from factories to storage (and energy as well) should be the lowest priority of all available jobs. Hauling from factory to weapon and storage to weapon is fine as the crew numbers are reflected based on the weapons, but factory to storage should be low priority because your crewmen would be prevented from doing more important jobs.