The Inside the Battlefield segment actually mixes up events from the first two GI Joe mini-series. Cobra Commander was arrested at the end of the first series, but was free in the second. He was arrested again at the beginning and almost immediately freed by Zartan after which he unleashed the Weather Dominatior. Cobra Commander managed to elude capture at the end of the saga.
The segment also shows Flint leading a ground charge on the Cobra fortress while in the actual episode he was piloting a fighter jet at the time.