New, Custom Campaigns and Levels that change things of the Vanilla Elements, such as replacing Weapons, Enemies, and Sounds, even though I think these changed Elements should've been their own thing. It should be illegal to change something from the Core Game without advertising the Changes, like come on.

LAByrinth: Requires several Mods that I don't necessarily like.
The Bastion of Darkness (The Damned Tower): It changes Sam's GERONIMOOOOO in TFE's Suburbs' final Secret (but why?).

Cry of despair monster sounds: Replaces the Base Enemies' Sounds, like the Kleers'.
Marine day atmosphere pack: The Map in question, which is also its own Mod, "Marine day", doesn't appear to have a problem, but this "atmosphere pack" did changed the Kleers' Sounds. I group them together for convenience sake, but again, seems like the Map is OK in that regard.