Why does the button make several gui instead of one?

You don't have a debounce in your client code.

You should add a debounce, into your client code; the debounce is to limit how often the function connected to the click event can be executed.

local ShowGui = game.ReplicatedStorage.Menu

local debounce = false;

script.Parent.MouseButton1Click:Connect(function()
	if not debounce then
		debounce = true;
		ShowGui:FireServer()
		wait(0.2);
		debounce = false;
	end
end)

Without the debounce, there is no telling how many times your script will end up firing to the server to create a new GUI.

To add, if the UI you are dealing with is only to remain over the client, then it is not necessary to execute cloning and such over the server. In FE local scripts can manage things such as UI (i.e. GUI, and sound), the client character's animation, and the client character's movement.

You should also be sending distinct information to the server from your ShowGui remote event if it is true that you are firing it for more than one purpose.

A remote event does not only fire the local player over to the server, it also fires some optional input specified by you.

Server:

local ShowGui = game:GetService("ReplicatedStorage").Menu

ShowGui.OnServerEvent:Connect(function(player, my_input)
	if my_input == "input" then --create a new menu only if the sent input is equal to the string "input"
		game.ServerStorage.GUI.TheMenu:Clone().Parent = player:WaitForChild("PlayerGui")
	end
end)

Client:

local ShowGui = game.ReplicatedStorage.Menu

local debounce = false;

script.Parent.MouseButton1Click:Connect(function()
	if not debounce then
		debounce = true;
		ShowGui:FireServer("input") --the input you send will tell the server that you want to create one menu whenever it recieves "input"
		wait(0.2);
		debounce = false;
	end
end)

Of course you can always change what input you are sending to the server and such.