I don't know for submarines but I've nearly crashed a scientific device because the sonar gave the false depth on our research vessel.

You have to set the sonar to a certain depth which you get from nautical charts. I don't remember the exact value but let's say that the digital nautical chart said 2000 m so the sonar was set to let's say 1500-2500 m. We deployed our oceanographic device when one of the officers double checked with an old nautical chart on paper and it said 1000 m. We've already been down for a few hundred meters when he called us to stop. We then slowly advanced and, believe it or not, the old chart was right. It was unlucky that the real depth was exactly half of what we initially thought it would be. Because of reflection the sonar gave us the way to the bottom and back to the surface as depth. If the officer hadn't listened to his gut feeling we would have wrecked equipment worth more than a big family house. That was off the beaten track though, far away from shipping routes - I think they should be mapped accurately by now. If the setting is correct, sonar gives you a good idea of what is down below. More detailed than satellites ever could.

But as I said no idea how that works with submarines. Maybe they didn't have the sonar on for some tactical or training reasons.