The Prospero Eel is not in the Fishing log. It is a quest fish only with no log or guide entry, just like the quest fish from the 60-70 SB fishing quests. The other fish you are talking about are facet delivery fish, not quest fish, which is why they show up in the log. It is not a bug, the fish is not missing and you don't need to and cannot catch it again. You are missing something else. You say you are missing sweetflesh oyster but think you've caught it just because you've crafted food that uses it. Have you caught it again just to make sure? Is the Sweetflesh Oyster in your Fishing Guide database? Go back to the Norvrandt Slope and catch another sweetflesh oyster just to be sure you've caught one.