I've discovered that its the heights of objects near the bee hive that causes the issue (which goes back to cover which everyone else is talking about).

For example if you build an 8 meter earthen wall around your base the beehive has to be at least 4 meters away from the wall for the bees to be happy. If you are trying to put that hive near a corner of an 8 meter high earthen wall the hive has to be at least 8 meters away from the corner of the walls with adjacent hives having less requirements but still more than 4 meters.

What this also means is that the bee hives have to be a meter apart from each other (since they are also a meter tall) or raised up one meter off the ground or the bees will not be happy until the neighbor hive(s) on the outside are filled with honey.

If you lay 9 beehives right next to each other (all most touching) on the ground like this:

OOO
OOO
OOO

Only the corner hives will be happy

OXO
XXX
OXO

Once the corner hives are full of honey the side hives will become happy but the center hive will still be unhappy until the side hives are also full of honey

FOF
OXO
FOF

You can prevent this issue by raising the hives off the ground by 1 meter somewhere in the center of your base where there are no other objects or by moving the hives so that they are at least half a meter away from the closest hive which will fix all but the center hive.

(This is the answer to Archdeacon Monseigneur's question. Full hives don't count against cover but when you empty the adjacent hives the crowded hives become unhappy until the too close hives are filled again. The cultivated earth issue is kind of a bug. If you plant walking forward the new plant in your "hand" will stay red until its far enough from the previous plant to be healthy and turn green if you try to plant it while its still red you get need cultivated earth error even though the earth is cultivated or you'll get blocked if you are trying to plant it too close to your avatar. This only happens when you plant walking forward. If you plant side to side or walking backwards the plants stay green, can be planted, and will have the plant is unhealthy label and then die. Walking forward is the only way that you can be certain the plants will always be healthy because you will get the error instead of being able to plant if it is too close together.)

Originally posted by Megahurts:

Odd. I have 3 hives indoors right beside my cooking station. They may not be happy but they still produce honey, so...

That's because floor tiles used as a roof do not count as a roof for cover. Only thatch or the darkwood shingles count