Modern filters dont show all used metadata values in the list/library
Modern filters don't show all 'used' metadata values in the list/library, metadata filter values are only shown if they appear on the first page.
Simply put if you have items not shown on the first page, their associated metadata values will not show in the filters meaning users wont even know they exist.
We cant use Modern views because of this, users keep reporting that they cant find items they know exist. its a total white wash...
We have a similar problem. In the Filter Pane we have several pinned columns to filter by. After using the filter once or navigating between views, many of the pinned filter columns do not appear in the filter pane. Usually a refresh of the page will fix it.
Modern filter functionality is also causing a lot of problems for us. When users click on the name of a group/tag in a library, it filters it in Modern to only see the files with that tag - beautiful! But then they click back to the default level of the library and the view is not showing all the documents, it's some kind of bug. Maybe there will be some groups there, some files, but not all. It can be resolved by refreshing the page or clicking the "All documents" view - but these are both workarounds. The actual way the libraries are designed to work is not working.