How can I "see" which media files Plex did not recognise?

What exactly do you mean?
Are you looking for files that Plex mismatched or incorrectly matched as versions of existing items – or are you looking for files Plex actually ignored by the scanner (e.g. movies named like tv-shows, unsupported formats…)?

WebTools/Export tools are still around – though they’ll only show you what files have actually been added to Plex.