Region3 stacking damage each time it's triggered?

remove the debounce, that's unacceptable, the real reason why he gets a lot of damage is because you subtract 3 health for every limb of the character, :FindPartsInRegion3 includes all the player limbs and accessories.

to solve this you can create container into which you are going to put players which have already been damaged in any limb, then, before damaging them with next limb you are going to check if the player is not already in the container, if he is then you won't damage him since he has already been damaged, otherwise put him into the container and deal 3 damage:.

local part = script.Parent 

local region = Region3.new(part.Position - part.Size/2, part.Position + part.Size/2)

while not false do
    local parts = workspace:FindPartsInRegion3(region, part)
    local already_damaged_players = {}

    for i, part in pairs(parts) do
        local char = part.Parent
        local player = game.Players:GetPlayerFromCharacter(part.Parent)

        -- table.find = hmm, i will find `player` in `already_damaged_players`,
        -- if he is there then don't run the `then` code!!!!
        if player and not table.find(already_damaged_players, player) then
            -- put the `player` into `already_damaged_players` since we will
            -- damage him on the next line of code
            table.insert(already_damaged_players, player)
            char.Humanoid.Health -= 3
            print(player.Name)
        end
    end

    task.wait(1) -- task.wait!!!!!!!! ):< (no strong reason why though)
end 

and nowadays Region3 is deprecated!!!!! roblox wants you to use Workspace:GetPartBoundsInBox, the choice is yours.....