Part creation and positioning?

Its because you was setting the Position of the head before clicking then the position of the X,Y,Z was the position taken when the script was running.

Here what I do its only Set the position to X,Y,Z when you clicking on the button and if already a part in the camera its will not create another.

The code here

local Player = game.Players.LocalPlayer
local Camera = game.Workspace.CurrentCamera

function Click()
    if not Camera:FindFirstChild("Part") then
        local X = Player.Character.Head.Position.X
        local Z = Player.Character.Head.Position.Z
        local Y = Player.Character.Head.Position.Y
        local Part = Instance.new("Part")
        Part.Anchored = true
        Part.Size = Vector3.new(2, 2, 2) 
        Part.CFrame = CFrame.new(X, Y+200, Z) *CFrame.fromEulerAnglesXYZ(-90,0,0)
        Part.Parent = Camera
        Camera.CameraType = "Scriptable"
        Camera.CoordinateFrame = Camera.Part.CFrame
        Camera.CameraSubject = Camera.Part.MenuCam
    end
end
script.Parent.MouseButton1Down:connect(Click)

You made your variables equal to properties (or actaully the properties of properties, but it's the same idea). This mistake is made a lot. See, when you do this, no reference to the object is kept. The variable will become what the property equals, but it will not change if the property changes later, and editing it will not edit the property. Again, this is because no reference to the original object is kept.

Your X, Y, and Z properties are numbers, and nothing more. It's the same as doing something like

X = 5
Y = 10
Z = 4

Make your variables equal to objects. Then you can access their properties.

local head = Player.Character:WaitForChild("Head")
----
Part.Position = Vector3.new(head.Position.X, head.Position.Y + 200, head.Position.Z)