To clarify, this is not a problem related to an underwater sound effect.
I am getting sounds in my video instead of the normal sounds, it sounds like something between underwater sound and a darth-vadery breathing. I am not using any time remaps in the layer with the problems. When I view the recording in VLC or other programs, it is fine, but as soon as I bring it into after effects it has this problem. I have also tried to render the audio separately in Adobe media encoder and it has the exact same problem.
Here is the video:
Before approximately 2:45 the audio is fine, then afterwards I switched recording software. The problem is really obvious at 7:50.