Do you think the navy has audio decoys on their subs? The kind that you can drop behind and remotely trigger to start making noise. It would go something like this:

1. Play a sound of a wrench falling (or whatever is the usual accidental noise).
2. A little commotion, may a few "Shh!"/panicked commands.
3. Regular sub sounds.

Number 1 would be a little louder to catch the attention of whoever is listening. You could also throw a small engine and computer to simulate real sub movements.