It might be annoying at first but it makes perfect sense. If you using a fusion rifle and the switch to a sniper the fusion rifle ammo you had isn't going to work and i sniper rifle.
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I agree that it makes sense that if I have a fusion rifle active and switch to the sniper that the ammo from the fusion rifle should not work in the sniper, but if while the sniper rifle is active I pick up ammo for it and then switch back to the fusion rifle that had ammo in it, it should not empty both guns, they both had ammo picked up for them and not fired. It just is not logical.
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Then you become to deadly and the game gets to easy there's a reason special ammo is limited ,all special weapons a one it kills if used properly and special ammo is dropped quiet frequently so there really is no need to have to special weapons full ,i have never ran out off special ammo while playing except when fighting a devil walker it that was because i was alone at the time.Just use it only when its needed and you won't have a problem.