Font Rendering Bug

Wrong font rendering for Nastaliq font (which is one of the most important fonts in Farsi language (persian) )
Someone told me maybe it's because some letters in this font made from two different glyph to make a new glygh.
This font is quite popular in Farsi language for using on Photoshop or using in Word Processors so there isn't any problem with the font itself.
He told me probably there is a problem with Kerning or Hinting.
He said those extra boxes under those letters are on glyph hinting area.
Actually i don't understand any of these things, maybe he's right or maybe wrong.

font link
https://github.com/RitaCo/WebFont-Nastaliq/tree/master/fonts

text:
بی به شکوه گفتم برم زدل