E2M6 has two untriggerable secrets.
The first and most obnoxious is this one:
It just shouldn't be flagged, as it's redundant with the larger secret sector next to it. Also it's apparently impossible to trigger even when noclipping in it.
The second is the doorway to the map. Since the floor of the map closet is slightly higher, your feet cannot touch the ground when your player mobj center is within the flagged, so you can't trigger it unless noclipping.
E2M7: again, two jabronis who can't get to the party. Though their curtain sectors do get triggered, so I'm not sure why they're stuck, all their friends managed to come. Perhaps they don't have enough vertical space to move.
E2M8: I was able to kill the boss and his minions without getting hit once. When running through the ending corridor with 200% health and armor, you can reach the end alive, and see some geometry you're probably not supposed to see. It doesn't last very long (I arrived there with just 20% health) but still. I suggest putting a walk-activated end level line a bit before just to be sure. With strafe-running, I was able to reach the end with still 70% health, enough time to take a screenshot.
E3M1: another secret that doesn't seem to register because your feet can't touch the ground when your center is in it. It's the teleport back to the starting area.
E3M1, continued: yet another pair of jabronis who miss the party.
Their problem is that the teleport destination thing is flagged to only appear on easy mode. Oops!
E3M4: a way to make the bridge work foolproof in GZDoom would be to to give a tag to sectors 120, 243, 244, 437, 438, and 439, and set up an invisible [wiki]3D floor[/wiki] for them.
E3M6: this platform has a damaging floor, which is quite inconsistent with the traditional "floor is lava" rules. (It's not like convection is simulated in any of the 23 levels I've played through before.)
Still in E3M6, the doggy tunnel is flagged as a secret even though the player can't step inside, and the room before it is already flagged as a secret anyway.
E3M7: I was hearing a monster and wondering where it was, as the area around looked perfectly clean. Checking with the automap and sure enough, there's a monster, but it's stuck in the void.
Still E3M7: there isn't a way to kill that bad guy who looks smugly at the burning death pit, is there? Do you still have some usable mobj you could repurpose for a version without the COUNTKILL flag, so that maxing is possible?