It's quite normal for calibre to bundle an HTM/HTML file into a ZIP archive. That way it can include any external file (images, ...) that the HTML code calls with links in the same archive file so that they can be handled as a unit.
I've never encountered one of these calibre created ZIP archives that failed to convert. In fact, I imported an HTML file yesterday and converted it to MOBI with no difficulty. Problems could arise if the HTML is improperly coded, but the fact that calibre "encapsulated" it in a ZIP archive isn't going to prove to be the problem.