I can delete files (notes) from the navigator if the Deleted files setting is set to the .trash folder or “Permanently delete”.
However, if the ‘Files & Links’ setting for Deleted Files is “Move to system trash”, then when i attempt to delete a file, it first briefly disappears, but then flashes back into existence.
Is your vault stored in a syncing folder, like iCloud, One Drive, Google Drive, Dropbox, etc? Do you access your vault with any other apps? Does it still do this if you turn off community plugins?