"B" Does not have any effect on metal spots in the sea. "M" works fine. EDIT: The ones placed by default can't be removed. If I press "M" then press "B" to delete that one, it works.
I have noticed this too. A hotfix right now for people struggling with this is to edit a text file (exported) version of the map (.pas? I can't remember) and remove the metal spots "by hand".
