Reproduction steps:
1) Load multiple scenes in the hierarchy

2) Double click the header of one scene to focus on that scene

3) Select a game object(for example "cube ") of ANOTHER scene and create empty parent
4) undo create empty parent

Actual Results:
Cube moved from its original scene to the focused scene

Tested on:

1. Unity Version latest main on neutron, Operating System (WIN10|MAC)
2. Latest trunk (6000.3.0a4), legacy Hierarchy

Note: when fix is done please check that it is also fixed on Hierarchy v2 (which can be Enabled on trunk in Preferences)