I had a problem with the way Construct 2 handles Mouse.X/Mouse.Y layout coordinates when scaling the layout. After some time I finally figured out a solution to this problem.
To convert the correct mouse position from the incorrect mouse position on a layoutscale that is not 100% you have to..
[System | Every Tick]
True Mouse.X = (Mouse.AbsoluteX-WindowWidth/2)/LayoutScale+Scrollx
True Mouse.Y = (Mouse.AbsoluteY-WindowHeight/2)/LayoutScale+Scrolly
I also have a HTML5 link and a *.capx file showing this.
The Blue Circle is Construct 2's Mouse.X/Mouse.Y position..
The Green Circle is the True Mouse.X/Mouse.Y position.
I hope this helps :)