By the rules of warfare you're not supposed to open fire on neutral flagged merchant ships unless they are ignoring your demands to stop and be searched (obviously a Ukrainian flagged merchant ship would be a legitimate target but I'm pretty sure no merchant ships flying Ukrainian flags are trying to run the blockade for that exact reason). Even then you're supposed to stop and rescue the crew if it looks like the ship may go down.Whilst I am not defending the action, I suppose it's reasonable to assume that any vessel going to Russian or Ukrainian ports in the black sea are taking risks and could be targets.
Interesting fact, the USA tried to convict the head of the German navy for his role in the U-boat sinking of US merchant shipping in the Atlantic, but he won the case on the basis that the US Navy did the exact same thing to Japanese merchant ships in the Pacific so it must be their policy too.