Now that you mention ships....I had a similar bug: When I brought a fleet ashore to disembark and it stopped right before the coast due to depleted movement points, the army stack appeared on top of the ships....and could no longer be moved because when I ended the turn a rebel stack appeared on the adjacent land tile. Pretty annoying because the army couldn't land or attack the rebels (out of any reason whatsoever) and I couldn't select the fleet under the army stack. The army tab was of no help so they stayed there until the end of the campaign (the rebels also did). Which wasn't far away anyway but it still sucked.
Generally movement with armies on fleets seems to be rather bugged, especially with respect to multi-turn landing operations.
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