Just had Raffi do this after an elite in N Drassen fired a burst from an Agram2000 at him and miss. He had been crouching, and had exactly the right APs left to fire one shot. The enemy fired during the enemy turn, I had just left Raffi the points in-case he got an interrupt, which he did not.
1) The game still recognized that it takes 30 AP in the 100 AP system for him to move forward one tile. So, technically the game seems to see him as prone.
2) The animation frame he is shown in, is slightly pointing downwards to the ground, as if he was standing and shooting at the ground in front of him.
3) I haven't tried moving him yet, I presume it will cost 30 AP to enter that tile, but I'll update and try that next.
Maybe although it says he is cowering, he is getting ready to flee LOL. Who knows? But yep this happened in latest 8646 exe build, to Raffi.
UPDATE: Although it thought he was cowering, using the R key twice brought him up to running stance with no AP costs, so there stance is unclear in actuality. The yellow figurine for showing where you will go shows as prone and the cost shows as 30 ap for that tile, but you can switch by R key to Running and it costs no AP, so the game is confused about his actual stance.
Hurl was PRONE, tried to HEAL HIMSELF in 8646. RESULT: He BEGINS HEALING, THEN CROUCH STEPS FORWARD ONE TILE DIAGONALLY and CANCELS REST OF HEAL. Seems possible that any task given to a PRONE MERC, may make it change stance. Not sure, but curious result. Or perhaps attempting to change stance due to a task results in some odd movement results in the current code.
If I make Hurl crouch manually first, then Healing works correctly. It was also true that Hurl was near 2 trees using those as cover to his right flank and he was pointing diagonally to the top of the screen.