What causes a script to not work after it is cloned?

Original works until it is the model is cloned.

--give cookie tray (put in inven, remove cookie tray, turn off oven
	script.Parent.ClickDetector.MouseClick:connect(function(player)
		local foodinventory = player:FindFirstChild("BakedGoods")
		if foodinventory ~= nil then
			print("yes")
		local alreadyexists = foodinventory:FindFirstChild("ChocChipCookies")
		if alreadyexists == nil then
			print("yeet")
			local tag = Instance.new("NumberValue",foodinventory)
			tag.Name = "ChocChipCookies"
			tag.Value = tag.Value + 12		
		else
			print("yoot")
			alreadyexists.Value = alreadyexists.Value + 12  --instead of making a new value, adds 12 to existing inventory value
			end	
		end
		
		workspace.Oven1.On.Value = false --turn off oven (will make oven w/player id tag attached later)
		script.Parent.Parent:remove()
		
	end)

Try this, if you disable the script before it is cloned, then enable it once it's in the Workspace, then it will work normally. Here is my example: Script within a Part, within a Model, within Workspace

-- give cookie tray, put in Oven, remove cookie tray, turn off oven
script.Parent.ClickDetector.MouseClick:Connect(function(player)
	local foodinventory = player:FindFirstChild("BakedGoods")
	if foodinventory ~= nil then
		print("yes")
		local alreadyexists = foodinventory:FindFirstChild("ChocChipCookies")
		if alreadyexists == nil then
			print("yeet")
			local tag = Instance.new("NumberValue", foodinventory)
			tag.Name = "ChocChipCookies"
			tag.Value = tag.Value + 12     
		else
			print("yoot")
			alreadyexists.Value = alreadyexists.Value + 12  --instead of making a new value, adds 12 to existing inventory value
		end
	end
	
	workspace.Oven1.On.Value = false --turn off oven (will make oven w/player id tag attached later)
	script.Parent.Parent:Destroy()
end)

I changed a few of the connections, for instance, remove is deprecated, and connect is now Connect. Script within ServerScriptService

while true do
	local model = workspace:FindFirstChild("Cook")
	if model == nil then
		local model2 = game.ServerStorage.Cook:Clone()
		model2.Parent = workspace
		model2.Part.Script.Disabled = false -- this is the location of the script with the above function
	end
	wait()
end

This doesn't have to be a continuous loop, but I used one to test that it works. You need to make sure that the script is disabled normally when in studio (since the function will enable it)