Actually, him stopping the railgun makes sense. He canceled the power that was pushing the coin that came from Mikoto. He can't do the same for Accelerator, since once the beams were launched, they were no longer "connected" to his powers.
Mikoto's railgun is like a push. She pushes the coin further. If she stops pushing (canceled), the coin returns to normal.
Accelerator's is like a throw. Once you throw something, it will travel according to the laws of physics. In base, AC's power just tells the object to "go that way".
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