Not necessarily. If the charts were properly updated and the pilot directed the vessel onto said uncharted hazard, then the skipper is probably gonna be okay. The board of inquiry will hammer the old man if there were any shortcuts, mistakes or gundecking of chart updates.
I use the Cape May Canal to take my boat between Delaware Bay and the Atlantic Ocean, and the waters off the ferry terminal at the Delaware Bay end of the canal are always tricky. You watch your depth gauge like a hawk and go very slowly, ready to throw the throttle into full reverse at the slightest bump.
That said, a harbor pilot ought to know this and ought to know where the ferries typically reduce the depth.