I had the same issue. I wrote this snippet to fix the bug for now -- hopefully it won't be needed in a later release.
I'm not using this fix in production yet and is specific to the popup event loop my map uses (which is a pretty standard one), so definitely test it in your application.
reactiveUtils.watch(
() => view.popup?.viewModel?.active,
(active) => {
if (active && !view.popup.selectedFeature) {
view.closePopup();
}
}
);