Those are glyphs with no Unicode points. There's no easy way to get them out 
of the normal version with the current script, which just takes ranges of 
Unicode numbers to discard. I know it's a little stupid to have them in the 
LGC version, but how is this tricking fontconfig? The normal code points which 
fontconfig should check, in the Arabic block, are all empty.

hmm for some reason selecting the glyphs and clearing them before generating lgc
in makelgc.sh doesn't work, yet it works in fontforge's GUI with the same
script. Besides some characters have different ID numbers or are absent in some
fonts.

I'll look into it.

(In reply to comment #1)
> Those are glyphs with no Unicode points. There's no easy way to get them out 
> of the normal version with the current script, which just takes ranges of 
> Unicode numbers to discard. I know it's a little stupid to have them in the 
> LGC version, but how is this tricking fontconfig? The normal code points which 
> fontconfig should check, in the Arabic block, are all empty.

Not sure.  Empty arab script perhaps.

$ fc-match -v 'DejaVu LGC Sans'
Pattern has 28 elts (size 32)
        family: "DejaVu LGC Sans"(s)
        familylang: "en"(s)
        style: "Book"(s)
        stylelang: "en"(s)
        slant: 0(i)(s)
        weight: 80(i)(s)
        width: 100(i)(s)
        size: 12(f)(s)
        pixelsize: 12.5(f)(s)
        foundry: "unknown"(s)
        hintstyle: 3(i)(s)
        hinting: FcTrue(s)
        verticallayout: FcFalse(s)
        autohint: FcFalse(s)
        globaladvance: FcTrue(s)
        file: "/home/behdad/.fonts/dejavu-lgc-ttf-2.9/DejaVuLGCSans.ttf"(s)
        index: 0(i)(s)
        outline: FcTrue(s)
        scalable: FcTrue(s)
        dpi: 75(f)(s)
        rgba: 1(i)(w)
        scale: 1(f)(s)
        charset: set(s)
        lang:
aa|ab|af|ast|ava|ay|az|ba|bam|be|bg|bi|bin|br|bs|bua|ca|ce|ch|chm|co|cs|cu|cv|cy|da|de|el|en|eo|es|et|eu|fi|fj|fo|fr|ful|fur|fy|ga|gd|gl|gn|gv|ha|haw|ho|hr|hu|ia|ibo|id|ie|ik|io|is|it|kaa|ki|kk|kl|ku|kum|kv|kw|ky|la|lb|lez|ln|lt|lv|mg|mh|mi|mk|mo|mt|nb|nds|nl|nn|no|ny|oc|om|os|pl|pt|rm|ro|ru|sah|sco|se|sel|sh|sk|sl|sm|sma|smj|smn|sms|so|sq|sr|sv|sw|tg|tk|tn|to|tr|ts|tt|tw|tyv|uk|uz|ven|vi|vo|vot|wa|wen|wo|xh|yap|yo|zu(s)
        fontversion: 190054(i)(s)
        capability: "otlayout:DFLT otlayout:arab otlayout:cyrl otlayout:grek
otlayout:hebr otlayout:latn"(s)
        fontformat: "TrueType"(s)
        embeddedbitmap: FcTrue(s)

Behdad Esfahbod 
Do you still experience this issue with newer drivers ?
Please check the status of your issue.