Bees are now disappearing, I suspect this is to do with them merging in to large stacks but only 2-3 are able to enter hives. At any rate, they started disappearing after they started merging so that is most certainly the cause. A number of quests are now very difficult to complete. Obvioulsy the honeycomb quest is difficult with all the bees gone. Pig breeding, sheep and mooshroom shearing quests are difficult now because merged stacks aren't being counted towards the count, and they are all merged now.
SUPPORT! I'm not sure if this is affecting survival too or not with stacking, but I really do not like how inconsistent or wack the stacking is