How to make this destroy itself, and only works if a player touches it?

First, tab your code correctly. It makes it much easier to read.

We just check if the thing touching is part of a person. The easiest way to check is if the touching part's parent has a "Humanoid":

local part = script.Parent
local EnemyGroup3 = game.Lighting.EnemyGroup3
local debounce = true

part.Touched:connect(function(touchingPart)
	if debounce then
		if  touchingPart.Parent
		and touchingPart.Parent:FindFirstChild("Humanoid") then
			debounce = false
			local Enemy = EnemyGroup3:Clone()
			wait(1)
			Enemy.Parent = Workspace 
			wait(120) --waiting 2 minutes before re-enabling
			debounce = true
		end
	end
end)

I am a bit confused as to what you mean by "it stays after you touch it."

Do you mean you want the button to vanish during those 120 seconds? I don't think that's the best way to communicate with players what is happening, since if they look for it they will not be able to find it during that period. Instead, just make it transparent or change color:

local part = script.Parent
local EnemyGroup3 = game.Lighting.EnemyGroup3
local debounce = true

part.Touched:connect(function(touchingPart)
	if debounce then
		if  touchingPart.Parent
		and touchingPart.Parent:FindFirstChild("Humanoid") then
			part.Transparency = 0.5; -- Indicate that it is disabled
			debounce = false
			local Enemy = EnemyGroup3:Clone()
			wait(1)
			Enemy.Parent = Workspace 
			wait(120) --waiting 2 minutes before re-enabling
			debounce = true
			part.Transparency = 0; -- Indicate that it is no longer disabled
		end
	end
end)