Originally Posted by Valloric
Sigil routes files into the correct folder according to the file's extension. Thus, JPG's, PNG's, SVG's etc. end up in Images; HTML, HTM, XHTML end up in Text etc.
Anything Sigil can't figure out ends up in Misc.
But if you added a file and it ended up in Misc, it should still be there after saving and then loading the file. If it's not, create a new issue on the tracker.
You gave the answer to the problem. I renamed the file LICENCE to LICENCE.txt and now it stays in the ePub. If it has no extension, it disappears. Don't know if this is a bug or a feature though