Spoiler:
after Atlantis started fighting the super hive they added another gate to the mix, the gate and custom DHD on Atlantis should have superseded the one on the hive ship, was probably just a writer glitch. this is what they should have done, they got to the gate but it wouldn't lock then mkay realized that Atlantis's gate was superseding it so Shepard decides to go back to the dart bay and fly a dart out of the hive with the others beamed into a storage device.
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