System Information
Operating system: Linux, Pop!_Os 20.10
Graphics card: GTX 1080ti

Blender Version
Broken: Blender 3.0
Broken: 2.65
Worked: 2.64

Short description of error
When using multiple windows that overlapped at the point of moving mouse from one windows to the other and then using some transform operations (scale, rotate) cursor will be present in inactive window at the point it was last registered.

Exact steps for others to reproduce the error

1. Open default scene.
2. Window -> New Window.
3. Resize window to make it smaller.
4. Hover mouse to main window, then back to new window. Preferably not too fast. Remember point where mouse crossed border from main to new window.
5. Optional: move new window away from that point.
6. R on cube. Notice there is now double arrow cursor in main window.
7. Switch to main window making sure that new window overlaps 3D Viewport of main window.
8. Select cube and move mouse to new window.
9. R. Notice that cursor appears in new window at point where cursor was.