Captains on the bridge, Captain probably had the conn effectively making him the OOD. Even if a junior officer was driving, Captain could have overruled him/her.

What Firetender noted goes back to an earlier comment that I made - this is an entirely new ship and type of ship for the CG. There will be a learning curve about how to make it work correctly. The error here is not having tried to switch from auto to manual before hand - like out in open water where the only thing they might run into was a wave, well before they had to do it "for real".

I'm sure driving a ship like the Baby Mac is an entirely new experience for the Captain and crew. It will take a while to learn how the various propulsion systems (like the azipod) affect handling.