When I encode from some lossless format with a cue-sheet to some lossy format using foobar, using single file output, Foobar2k seems to use the cue-sheet's name rather than the names indicated by the information in the cue-sheets.

Is there some way to fix this?

If not, I think it would be a nice feature to add in future versions of Foobar2k.

You can use placeholders like %artist%, %album%, %title% and so on in diskwriters 'Output filename formatting' settings.