Bees will take damage if they fly to close under a solid block.
They don't take damage if the block is a half slab, stair, or other "incomplete" block.
They also don't take damage from glass and leaves, but will take damage from ice, glowstone and sea lanterns, despite the fact that all of these block are considered transparent. Any "complete" block that is opaque not mentioned here will cause damage to the bees.