From the manual:
Return the position of the mouse cursor in game co-ordinates. This is (0, 0) at the top left of the layout. It changes to reflect scrolling and scaling. However, if an individual layer has been scrolled, scaled or rotated, these expressions do not take that in to account - for that case, use the layer versions below.
Return the position of the mouse cursor in game co-ordinates, with scrolling, scaling and rotation taken in to account for the given layer. The layer can be identified either by a string of its name or its zero-based index (e.g. Mouse.X(0)).
i.e. use Mouse.X("Layer 0") and Mouse.Y("Layer 0").