This is an issue I've noticed for awhile, but investigated and found a fix today. Notice in this gif how the bone handles also render in the inspector randomly:
This is due to SpineHandles not checking if (Event.current.type != EventType.Repaint)
when drawing its meshes and other rendering calls. Note this is how Handles works internally: https://github.com/Unity-Technologies/UnityCsReference/blob/0aa4923aa67e701940c22821c137c8d0184159b2/Editor/Mono/Handles.cs#L354C5
I was able to fix this by checking if the current event is a Repaint in each OnSceneGUI call in the Spine editor code, but it would probably be a better fix to check it in SpineHandles similar to how the Handles class works.