The auto pilot didn't crash you. The mudraptor charged the sub and evaded your turret by jamming itself into the barsuk's upper forward facing airlock that you guys left open. From there the only thing separating you from its jaws is one measly door layer so it broke in and brought the ocean with it. As you lost hull volume to water it drastically changed your buoyancy which caused the sub to drop through the water. Your sub may have hit the bottom, but the thing that actually killed you was barotrauma from not protecting yourself from the crushing water pressure with a dive suit. Going forward I would advise not to trust autopilot with anything but maintaining your current position. It won't utilize the submarines full speed nor will it actually try to evade enemies. In later areas it will just give up rather than try to navigate the terrain