It's a minor bug if the document contains only one Layer Comp. It can be easily solved by opening the script file located in the Photoshop application folder Presets>Scripts>Layer Comps To Files.jsx
Change line 167 from:
if ( compsCount < 1 ) {
Save the script and run it again.
Though, if there's only one comp in the file, it's just as easy to use File>Save As... 🙂