I think you stumbled across an unhandled special case there. Tried to reproduce by adding a non-extension text file as a new book. The book got added, and the file copied to the library (checked in file manager), but no format entry was created for the book. Conversion and viewing thus wouldn't work, since there was no format entry. Interestingly enough, the file got deleted okay when I deleted the book, although it may be that calibre just wiped the entire directory.
Practically speaking, I don't think there's anything you can do about it other than appending the extension to the files. This calls, in my eyes, for one of the developers to step in- I think something in the order of a dialog box stating that the file is of unknown format and asking the user to manually specify the format would be an elegant solution.