@vikkturr88 When the final wave spawns, there are usually two ships. One of them has the loot (4 skele chest and 4 skele skulls). However, to get the commendation, you need to kill both of them. Sometimes the other one takes a bit longer to spawn (once it spawned after we killed the one with the loot).
My advice is, if the music isn't gone, the battle isn't over. You have to hear the trumpets after a successful battle. If you still hear the "action" music, move around a bit in the area, maybe you are in a place where the second one can't spawn.
EDIT:
The commendation progress for sunken ships goes up one by one ... you don't have to finish the battle to get some progress