Was able to track down why the warning is being output and we'll need to make some improvements to our API as some function calls are going directly to Joomla user object, but they should first go through CB user object that maps to Joomla user object to avoid this.
forge.joomlapolis.com/issues/8166
We'll review improving this for our Joomla 4 implementation as this could become more common. Normally that clean up behavior should clear those though and seams to be working as expected in my tests so am unsure why it didn't clean up for you.