As I was thinking about running 100% easy, I remembered that there are two levels that have enemies that either don't spawn or are out of bounds, which are Security Complex (Mission 2) with 2 missing (30/32), and Research Lab (Mission 4) with 1 missing (37/38).

My bet is the 2 missing enemies (3 on hard) on Security Complex are Flyiers that, for any given reason, never spawn. There's stil some inconsistency, since some people missed 2 on hard (instead of 3). What is consistent is the only missing enemy on Research Lab since, on any given difficulty, it is always just 1.

How should we settle this to run 100%? I found that 1 missing enemy on Research Lab is consistent, but it's a bit harder for Security Complex, since we have no way to guarantee that there will be missing 2 enemies every single time (at least on hard, where 3 could be missing).

---Edit---

I watched both DarXtar Slayer playthroughs and I found out that there's an Enforcer that spawns on Security Complex that everyone misses (included me) (). After taking him out, the counter goes up to 31/32 on easy (same in medium), or 39/41 on hard, making it 1 enemy missing on easy (and medium) and 2 on hard.

This rules out any inconsistency on Security Complex. Unless we either find proof somewhere around or we experiment enough to find them, 100% should be considered 1 (easy, medium) and 2 (hard) kills missing on Security Complex, and 1 kill missing on Research Lab (all three difficulties).

---Proof---

I found this old thread where they state the 2 enemies on Security Complex are missing on hard too. Strange enough, someone claims to only miss 1 enemy. It is the only instance I found where only 1 enemy is missing on Security Complex (https://gamefaqs.gamespot.com/boards/198379-quake-ii/50612342).

On this 100% hard playthrough (), DarXtar Slayer missed 3 enemies on Security Complex (39:12), and 1 enemy on Research Lab (1:30:02). He did another 100% hard playthrough, this time with a mouse (). He missed 2 enemies on Security Complex (38:13), and 1 enemy on Research Lab (1:25:54).

On this 100% hard playthrough (). doomer2012 missed 3 enemies on Security Complex. He didn't finish the game, so we won't know how many enemies missed on Research Lab.

On this 100% hard longplay (), while Mad-Matt (World of Longplays) missed enemies on another level, he missed 3 on Security Complex (54:03), and 1 on Research Lab (1:53:59)

On this 100% hard longplay (), AlexanderGhost missed 3 enemies on Security Complex (1:02:38), and 1 on Research Lab (2:22:17).

On this medium playthrough, elbryan42 missed 2 enemies on Security Complex (), and 1 on Research Lab (). He then replayed the game on hard, and this time missed 3 enemies on Security Complex (), but didn't reach Research Lab.

On this hard playthrough, BlazeRed missed 2 enemies on Security Complex (), and 1 on Research Lab ()

On this hard playthrough, Death Ninja missed 2 enemies on Security Complex (), and 1 on Research Lab. The counter said he missed 2 because he left alive the tank at the end of the level ().

On this hard playthrough, Black White missed 3 enemies on Security Complex (), and 1 on Research Lab ().

On this hard playthrough, BaronOfStuff missed 2 enemies on Security Complex (), and 1 on Research Lab ().