This has been an issue that's well documented, but the staff don't seem to have the time to put in to properly research it.

Bees that are kept in captivity, completely enclosed spaces, are despawning without any player input. They seemingly just vanish from the game after a long time, with no indication of death. 

I can't say for sure how long it takes, but we had bees in a greenhouse to farm honey, completely closed off. They worked there just fine for a few IRL weeks. Within the past few days I realized that the bees were gone. Poof, vanished. No rhyme or reason as to why they're gone.

The bees are kept in a structure with no water, and campfires covered by trap doors. They have flowers to pollinate and more than enough hives and nests to house them... Yet they are just gone.

Several chunks away, another players' bee farm is also stripped of their bees. This has been a bug since the bees were introduced into the game and it's insanely frustrating to deal with. The hives and nests are totally empty, too.

The only way I know to reproduce this is just playing over time or leaving the area(s) multiple times. It happens in all three playing options - single player, multiplayer, and realms.