It is quite the opposite from what you are arguing. China is responsible for the conduct of the vessels they allowed to fly their flag.

They can later claim that the crew and captain acted on their own will, without orders from the Chinese leadership. They can duly punish the captain and crew or disavow the vessel and declare them renegade, disallow them to fly their flag. But without such a declaration, a nation such as China is responsible for the conduct of their fleets, be they civilian or military. And any vessel they allow to fly their flag is part of their (in this case civilian) fleet.