I have a setup that seems to have been resolved in an early bug fix but is still happening. I have 5 hives in an area and campfires under all of them with a trap door between them. All the campfires are between 5-6 blocks under the hives and all have a hay bale under. Bees still get mad when I shear the hive.
Please check MC-164336 and see if any of the info there fixes the issue you have.