After you close the popup, try highlight.remove()
FeatureLayerView | API Reference | ArcGIS API for JavaScript 4.24 | ArcGIS Developers
I didn't highlight any feature,so highlight must be null. the highlight is automatically by popup's behavior.
Not sure why the highlight problem is occuring if your code didn't set it, but the highlight is attached to the layerview, maybe if after you close the popup you set the view.layerview.highlight.remove()?
If you have a sample repro in codepen or github, would be helpful to track down the issue.
This sample works as expected when the popup closes via view.popup.close()