Thank you for reporting a bug to Unity.
Our investigation indicates the issue originates from the user code, rather than Unity itself. Because the problem lies outside our codebase, we're unable to address it directly.
In the current report, the user is calling Handles.SphereHandleCap.
This function should only be called during events corresponding to the last parameter assigned to it (in that case repaint events). Adding a check on the event type before calling it fixes the issue:
" if (Event.current.type == EventType.Repaint)
Handles.SphereHandleCap(..,EventType.Repaint);"
This has to be done this way as the method can also be called during Layout/MouseMove events to calculate handle distance to mouse.
We cannot change this in the method itself at the moment as it could introduce regressions to certain user projects. However, this element is definitively lacking at the moment in the function documentation and I'll see to update the documentation accordingly.
We will close this case as 'As Designed.' If you have feedback on how the feature could better meet your needs, please let us know - we value your input and consider it in future improvements.