Quote Originally Posted by Mouzafphaerre
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A battlefield workaround that works sometimes is repeatedly (double-clicking madly) ordering your soldiers to run elsewhere and once they're out of the buggy loop order them to walk up the tower again. If ordering towards a certain location doesn't work, try another..
That's what I do. Once the siege tower is placed and if they get stuck, just highlight the unit and click on the top of the wall, a few of them at a time will get unstuck and start climbing the tower. Repeat until the entire unit is up the tower.

The annoying thing is when this happens to the computer because the unit will sit there the entire battle. That's when you move phalanxes in and chop 'em up.