Honolulu-based Matson Inc. has agreed to pay a civil penalty of $725,000 to the U.S. Environmental Protection Agency over federal Clean Water Act violations relating to a molasses spill in Honolulu Harbor in 2013. This follows a July 2015, settlement, in which Matson (NYSE: MATX) paid $15.4 million to the state of Hawaii over the spill. In October 2014, Matson (NYSE: MATX) paid a $400,000 fine to the state plus restitution of $600,000 divided up between the Waikiki Aquarium and Sustainable Coastlines…