I recall the same thing happened in RTW in bridge battles when the enemy tried to cram too many units across the bridge. I recall making a custom battle with a few elite units with max armor & experience versus three armies of low level troops. Framerate was fine until they all tried to cross the bridge at once. The framerate tanked because all those men were constantly changing direction and walking into one another while trying to find an open path to the other side.
I agree with hoom, it's definitely a pathfinding issue; all those men constantly trying to find alternative routes to get up the ladders and siege engines are sucking up CPU cycles.
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