Sometimes after death of Zombieman (Shotgun?) his sprite remains standing in the same place forever. These kill not added to kills counter, not allowing you to get 100% kills in a level.
Happens only 2 times for entire playtrough for me.
More often happened that Lost Souls is not count (without any sprite in map, tested it with cheats).
In "Map 17: Watch Your Step" I closed exactly 1 Lost Soul that stayed after Pains Elements in center room. I looked on automap with cheat: LS still was in the room. Then I closed the automap and walked in level for a dozen of seconds and opened map again - LS disappeared. And i was not able to do exactly 1 kill for 100% kills, there was not any more enemies in map (tested again with cheats).
I am really not sure, but for me looks like only LS from Pain Elementals affected by this bug.
In "Map 17: Watch Your Step" I closed exactly 1 Lost Soul that stayed after Pains Elements in center room. I looked on automap with cheat: LS still was in the room. Then I closed the automap and walked in level for a dozen of seconds and opened map again - LS disappeared. And i was not able to do exactly 1 kill for 100% kills, there was not any more enemies in map (tested again with cheats).
I am really not sure, but for me looks like only LS from Pain Elementals affected by this bug.
Happens ~6 times per playthrough. Used build from https://doom64ex.wordpress.com/