Typical Arabic fonts usually have some deficiencies in displaying Quranic texts. Some of these issues are listed below.
In most Arabic fonts, when Kasra is combined with Shadda, Kasra is displayed above the base line, just below the Shadda, which might cause it to be mistaken by Fatha. For example, in the word ذُرِّيَّة there is a Shadda+Kasra above Reh, while there is a Shadda+Fatha above Yeh. The distinguishing difference is that in the combination of Shadda+Fatha, Fatha is put above Shadda, while in Shadda+Kasra, Kasra is below Shadda. The same issue applies to the combination of Kasratan (tanween) + Shadda.
To fix this issue, you need to use advanced Arabic fonts, such as hafs and me_quran, that always display Kasra below the base line even if it is combined with a Shadda.
One of the oldest standards for Arabic encoding called “Arabic-1256” does not have any code-point for Superscript Alef which is necessary for representing a complete quran text. As a result, some older Arabic fonts do not include Superscript Alef by default. If your font has problem with Superscript Alef, you need to either change your font or update it to a newer version.