Whenever I launch ntt it makes a bunch of random sounds such as shooting bullets, frog sfx, and horror, sfx. When in game all of the sound effects are jumbled, such as freak sounds for desert enemies.

That means that you are patching a different version of Nuclear Throne - depending on what it is, you may want to use modbranch_2021, or use ntt_development (which is currently distributed as-is on Steam)