Phobos Anomaly: Because the final room "kills" the player, obtaining all the kills in this room is quite difficult to do. Normally, 63% kills is considered the normal "maximum" in competitive Doom, even though more than that can be obtained by quickly getting some kills in the final room.
Sever the Wicked: In the first version of Doom 2, Map 25 (Bloodfalls), which was Shawn Green's first map he designed, has 0 secrets. In later versions, it has 2 secrets. Infamously one of the secrets in that map is an empty room on Ultra Violence and Nightmare (on lower difficulties, it contains a BFG). Once again, we have a Shawn Green map with some hilarious broken secrets. Likely due to a poor copy and paste job while designing the map, 18 stairs in a row are tagged as secrets, plus the room at the top with the megacharge. These can be obtained normally, but it's hilariously dumb. However, right before these, there are two torches that are tagged as secrets. You would have to literally step inside the torches to tag these two secrets, so they can only be obtained with the idclip code.
And Hell Followed: There are two secrets at the same location that involve an invulnerability sphere. The door that opens to the invulnerability sphere is too thin for the player to tag, and the ledge to the invulnerability sphere is too high up to stand on. Both of these must either be tagged via the idclip code, or by using the Cyberdemon's rockets to boost you onto the ledge. The door itself 100% requires idclip to tag.
Industrial Zone: The speedrunner, Zero Master, found a way to obtain this secret only a few years ago. One of Doom's creators and map designers, John Romero, even tweeted about it when it was discovered. There's a portal on a ledge that's too thin for the player to normally stand on and tag the secret. There's a hilariously dumb way to tag it by luring a pain elemental all the way to the portal, and having him spawn a Lost Soul "into" the player. This pushes the player ever so slightly backwards, just enough to tag the secret. This secret is not considered necessary for 100% speedruns, as until a few years ago, it was deemed impossible to trigger without the idclip code. Even now, it requires a painfully slow method of luring the Pain Elemental all the way to the portal.
Monster Condo: There's a secret that's only obtainable in the first 30 seconds of the map. After that, a wall closes over the area and it cannot be obtained. This is by design though. As long as the player is aware of it, it can be obtained normally. You just have to get to it as soon as the map begins. However, there is another broken teleporter secret in this map that isn't considered necessary in 100% speedruns. It IS possible to tag this secret with a very precise wall-running technique, but it is quite difficult to do.
Hunted: There's two exits at the end of the map. The one on the left just ends the map normally. The one on the right brings you into a room with a damaging floor and 4 Arch Viles. Much like the end of Phobos Anomaly, this map ends with the player "dying" or close to it. It's nearly impossible to kill the final 4 Arch Viles, even with a BFG shot. These 4 kills are not considered necessary for 100% completion, as they are EXTREMELY unlikely to obtain before the map ends.
Dead Zone: The Cacodemon and Pain Elemental behind the outer wall cannot be accessed normally. I believe something was SUPPOSED to trigger this wall to lower, but it never does. The only way to get them to come out is by hitting any floating enemy ABOVE their location with the rocket launcher and hoping that the splash damage hits them, forcing them to emerge. However, this is tricky to do, requires a fair bit of luck, and these two kills are not currently deemed necessary for 100% completion in competitive play.
