When I opened a file in my desktop folder, it asked me what program to choose as default. (It was a new format.) I chose 'xarchiver', which did not work, because it's not an archive. The problem: Upon rightclick on the file, 'xarchiver' did not show up in the context menu; only "Open With Other Application...", but that only opens xarchiver. Now all files with 'unknown' type do not open the chooser, but 'xarchiver'. When bypassing this with choosing an application to open it with in the file's properties, everything works fine with files of it's kind. When other applications work, it would be a bug with xarchiver, but I can't test this, since I don't know, where the files, which assign apps to files, are. meow.
This is something we probably can't fix in Thunar itself. We are planning a dialog to edit file associations globally though and that would help in fixing things if some association needs to be reset. I'm thus closing this bug as WONTFIX. You can solve your issue by editing ~/.local/share/applications/mimeapps.list and removing the line application/octet-stream=... in the section called "[Default Applications]".