The Arabic alphabet was fixed for a language whose consonant inventory has since changed, and it has not been revised to follow. Several letters that stood for distinct sounds in the language the grammarians described are now pronounced identically in most places where Arabic is spoken. Za and dad have merged across much of the Arab world. Tha and dhal have merged with ta and dal, or with sin and zay, in the settled dialects of Egypt and the Levant while remaining distinct in the Gulf and in bedouin speech. Qaf is a glottal stop in Cairo and Damascus, a hard g in much of the Gulf and Upper Egypt, and a uvular stop in careful reading everywhere.
None of this shows in the spelling. Written Arabic keeps every letter, and a word is spelled according to its form in the standard language whatever a given speaker does with it. The result is a script that records a phonology no single community speaks, which is exactly what a script shared across a very large area has to do if the writing is to remain common property.
For the religious tradition the consequence is direct. The Quranic text is recited, not merely read, and the recitation is governed by a body of rules that specifies the values the letters carry in that setting, independent of local speech. A reciter in Jakarta, in Lagos and in Rabat is taught to produce the same distinctions, and the merged pairs of ordinary conversation are held apart. The written page does not enforce that; the chains of teaching do.