I did some testing this morning with my savegame. I can reproduce the "missing zombie" but it remains somewhat unclear why sometimes a zombie spawns from a civilian after a reaper attack and sometimes not.
It could be connected to how far my soldiers are away from the location. If one of my soldiers is close to the location a zombie will spawn with 100% chance. If none of my soldiers is within reach of the location where the zombie should spawn, it will almost certainly not spawn.