I already had this problem and asked in the forum, but ok that was 2 weeks ago, it might be hard to find.
The issue is logical, because coordinates get scale in the layer (to conserv relative position between elements).
I was surprised by the answer 'cause it looked like a hidden feature of c2 and is actually quite interesting.
If you want the mouse position projected on the layer that is scaled :
Mouse.X("layerName") or Mouse.X(layerNumber) (same for Y of course)