I had that happen to me as well. I had to move out of the square and then back in to get the loot. Annoying.

THings get even more bizarre when you have a skill or spell that can convert an enemy, such as 'Tame' which comes with the Beastlord profession and enables your sovereign to convert beasts such as wolves and spiders.  If your sov's army is maxed out and you convert beast(s), each beast will get its own army -- no big whoop -- but they then appear at the location where they were when you attacked them (or they attacked you).  This has a potentially big oddball effect if there was more than one enemy army present at that location, as the troops (beasts, or other) you converted and are on your side will co-occupy a tile with an enemy!

Me too, with beasts and loot.