Oh so any files in vgafonts that are in the misc directory, you want moved out of vgafonts and into misc? Use the wildcard to select all files with a * like this:
mv /usr/X11R6/lib/X11/fonts/misc/vgafonts/* /usr/X11R6/lib/X11/fonts/misc/
Without the /* at the end of /usr/X11R6/lib/X11/fonts/misc/vgafonts your trying to actually move the whole directory of vgafonts to misc, where it already resides. Hope it makes sense to you now to accomplish the move?