That depends if you’re referencing the position in the global coordinate system (which you are probably doing) or the viewport coordinates
See here my little demo that shows the difference between the two:
The first label prints this position:
text = "viewport coords: " + str(get_viewport().get_mouse_position())
The second label prints this position:
text = "global coords: " + str(get_viewport().get_camera_2d().get_local_mouse_position())
Here’s the scene structure, you can see the Controls are centered in the global coordinate system:
