So, I'm not sure if the system is supposed to be acting this way but ever since the Skelly Sloop update about 80% if not more of my encounters with Megs and Krakens have also spawned a Skelly Sloop at the same time which makes them an absolute pain due to conflicting strategies.
Additionally, about a third of the time I kill one of the two (usually the Skelly Sloop) when they spawn together they fail to spawn any loot drops when defeated. I can't be as sure about the others since if the Skelly Sloop isn't the first to die you usually loose track of where the treasure should be.
