As per MC-255199, which is an intentional behavior, Bees don't instantly incur damage upon contact with water. Instead, there's a brief delay before they begin taking damage. However, this countdown is reset when the world is reloaded. Consequently, upon reloading the world, Bees will experience the delay before taking damage again, even if they were already taking damage before the reload. The issue lies in the fact that this timer isn't saved to NBT.