The Semitic languages characteristically keep a set of consonants made deep in the throat, the gutturals, and they are among the first sounds to weaken when a language changes. In Mandaic they weakened early and thoroughly, and that is one of the features by which the language is identified and set apart from the other Aramaic dialects.
The consequences are visible in the alphabet. The eighth letter, it, stands where Aramaic, Hebrew and Syriac all have heth, and the modern character standard describes it as a pharyngeal while the letter's reading in the spoken language has moved a long way from that classical value. The sixteenth letter, in, stands where the others have ayin and is read in Mandaic as the vowel e as well as carrying the old pharyngeal value. Ah with the affrication mark supplies a pharyngeal that the plain letters no longer deliver.
So the script has ended up recording, with marks and with shifted readings, a set of distinctions the language itself has largely let go. That is not decay and it is not confusion. It is what happens to a liturgical language: the classical spelling is preserved because the texts are preserved, while the spoken descendant goes its own way.
Neo-Mandaic, still spoken by a very small number of people, is that descendant. Its relationship to the classical language written in these letters is close and is not identity.