Bees have code that makes them take drowning damage if they are inside water for 20 ticks. The problem is; this triggers without them being submerged, as they start to take damage if they hover just above the water surface. This causes free-roaming bees to just kill themselves over time if there is water nearby.
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We're tracking this issue in MC-190261, so this ticket is being resolved and linked as a duplicate.
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Bees will take damage when coming into contact with water and I'm pretty sure this is intended, therefore leading me to believe that the core issue here is that bees sometimes don't always avoid water when pathfinding, thus making this a duplicate of MC-190261.