(Read Body Because Title was too long) How do I fix this?

Try destroying the humanoid's body parts to prevent them from touching when the player dies:

game.Players.PlayerAdded:Connect(function(player)
    local character = player.Character or player.CharacterAdded:Wait() -- if the character doesn't exist, we'll wait until it does
    local humanoid = character:WaitForChild("Humanoid")
    humanoid.Died:Connect(function()
        for _, bodyPart in pairs(character:GetChildren()) do -- loop :GetChildren() to destroy them all
            bodyPart:Destroy() -- destroy the parts
        end
    end)
end)

Hope this helps!

One solution for this problem is to have the checkpoints detect if the player is dead. So like when the checkpoint is touched make sure ..Character.Humanoid.Health > 0 to set their checkpoint. This should do the trick!