I can confirm that. I couldn't find a workaround.
Also, something similar seems to happen with fleets. I had a naval battle near a trade spot. There were other (neutral) fleets around. After winning, some captured bune ended up (in one stack) on the same spot as a neighbouring fleet. This captured stack became un-movable (the cursor turns into a red X).
Anyway, these are the only 2 bugs I've encountered. The strange black skies and completly transparent water and coloured flares I experienced when first playing went away after upgrading to the latest Nvidia drivers (I own a GeForce 9800). The game seems to be enjoyingly stable (minus a couple of ctd's or so) and a million miles away from the vanilla ETW (that almost drive me insane with crashes).
Bookmarks