I re-watched the scene where the Woodbury people were in the prison. There were flash bombs in closed spaces, alarms blaring (keeping in mind these people probably have gone a year without hearing mechanical sounds), zombies approaching and the resulting gunfire. All it takes in that panic for one person to yell "Let's get out of here!" and they would all follow.
Then they go outside and are being shot at- time to get out. I think the Gov thought they were going to fall back a bit and re-group; not a full on retreat.
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