I ran an experiment. I brought in another (untamed) boar and led it to the bee hives. I had a set of stone stairs but have taken them down since. The boar aggro the bees even in the rain where they are not flying around and eventually killed the boar. The one bee hive was damaged in the process. Although this all happened when I was not online or when I ran in and just headed inside and didn't notice for it was late and went offline.. but I think now Frank aggro the bees (even if he was tamed) and probably ran down to the pen area, bringing them there before back and killed. The bees then went after the other boars, if that is possible.. but they were all dead inside the pen up the end closest (at a distance) to the bee hives. The bees also attacked my character but did little to no damage, they mainly went after the boar.

I've thank everyone who gave input for this mystery.