Why dose my script work at first then stop working?

Have you tried separating that over 50 jump clause? It could be that once it hits 50 jumps, the gui just keeps playing, rather than an increase in the jump value. Try this:

local plr = game.Players.LocalPlayer.Character:WaitForChild("Humanoid")
local debounce = false
local debounce2 = false
local Jumps = game.Players.LocalPlayer.leaderstats
local JumpCounter = script.Parent.Parent.Jumps
local Sound = script.Parent.Parent.Sound

plr.Jumping:Connect(function()
    if not debounce then
        debounce = true
        Jumps.Jumps.Value = Jumps.Jumps.Value + 1
        JumpCounter.Text = Jumps.Jumps.Value

        if(game.Players.LocalPlayer.leaderstats.Jumps.Value >= 50) then
            Sound:Play()
            wait(3)
            Sound:Destroy()
            script.Parent.Parent.Frame.Visible = true
            script.Parent.Parent.Frame.Trail1.Visible = true

        else
            script.Parent.Parent.Frame.Visible = false
            script.Parent.Parent.Frame.Trail1.Visible = false

        end
        debounce = not debounce
      end
  end)

if(game.Players.LocalPlayer.leaderstats.Jumps.Value >= 50) then
if debounce2 == false then
debounce = true
            Sound:Play()
            wait(3)
            Sound:Destroy()
            script.Parent.Parent.Frame.Visible = true
            script.Parent.Parent.Frame.Trail1.Visible = true
debounce2 = false
        else
            script.Parent.Parent.Frame.Visible = false
            script.Parent.Parent.Frame.Trail1.Visible = false

        end

Instead of debounce = not debounce do debounce = false