How to get past the box
Here are spoilers for how to get into the tunnel below.
After you enter the tunnels by cutting the chain, you’ll likely find yourself blocked by a box in the water. It’s not a bug: to progress, you have to pump the water out. Make sure the generator is on, and then flip the power box in the room (near the stuck box, at the end of the room on the left). Go back to the tunnel entrance next to the door you came from (where you cut the chains), and flip the switch on the machine (it’s a pump) to pump out the water, and you can progress.
I got stuck here thinking it was a physics bug, since it looked like the box could be pushed out of the way, and I didn’t understand that the machine at the start of the room was a pump. I thought it was a mini generator to power the tunnel area, or something, definitely didn’t think it was a pump. I tried to fuel it up before going forward, but I couldn’t do that, so I just ignored it and when I later flipped the power box, I didn’t think to go backwards.
Maybe I just had a dumb moment here, but I was lost here for longer than I’d have liked. Hopefully this reaches and helps at least one person who also got stuck here.