[Lower Deck]

Maybe a partially sunken shipping container. Thousands are lost at sea every year.

I would assume the submarine would have been at a depth of several hundred feet. Way too deep for a shipping container.

[Lonesome in Massachussets]

I would assume the submarine would have been at a depth of several hundred feet.

The South China Sea is shallow and not an ideal submarine operating area. They were obviously there to sniff around at the Chinese Navy, and the Chinese may have deliberately interferred with their mission. It happens.

[Blood of Tyrants]

Not necessarily. It is possible for a shipping container to naturally achieve neutral or near neutral buoyancy and sink slowly.