First issue: it's possible to upload both a folder and a file with the same name to a given repo. My user has uploaded both:
somedir (extension left off so name collides with directory created when uploading previous file)
Second issue: When deleting the file by clicking Delete asset through the web interface, the directory disappears from the interface. However, the assets contained still exist, and can be accessed by requesting them (like somedir/somefile.zip example above). New uploads can be submitted, but do not recreate the visible folder of somedir to correct the erroneous loss of the folder through the above.