I've seen this happen a few times.  This time there was an enemy peasant (you can see that unit's card in the pic) that I tracked through the woods.  I couldn't see the unit as it moved thru the woods, but could follow its movement by holding the cursor over its location the cursor, getting the 'crossed sword' cursor.  In the pic below the 'invisible' enemy peasant is on the farm tile (where the movement 'X' is -- the cursor didn't show in the printscreen). You can see the enemy peasant's card (which shows when holding the cursor over its location) and in it it mentions that unit is targeting Bannor Highsley, who I recruited and is in my army with my Sov to the right of the foe.

I see this occasionally.  One example being I had a small stack of troops and it was wiped out by a troll.  The troll ended up in the same tile as my stack and it was invisible.  Holding the cursor over that tile changed it to the 'crossed swords' cursor.  I tried to get a pic but got the DX crash when TABing. 

Reloading seems to fix this.