I often see dead armies remain on the screen until next turn, so I am conditioned to ignore armies that appear to remain on a square after I have attacked and killed them. Decoys.
But I also regularly see and 2nd/3rd/4th (etc) army on a square go invisible after I kill the first army on that square. Steath. And especially easy to fall for because of all the decoys.
A bit or guesswork long-distance debugging -- if there's a piece of code somewhere that goes something like "if the number of armies on this square drops to zero, erase the army graphic and show the background landscape" then someone has their "= 0" and "<> 0" confused. (That's cobol conditional, not C).
Anyway, its an OLD bug. Used to see it in WoM too.