Three of the twenty-two letters, tit, tsaadiy and quf, belong to a series that has no equivalent in English and that sets the Semitic languages apart from their neighbours. They are usually called emphatic, and they pair off against plain consonants: tit against taaf, tsaadiy against singaat, quf against kaaf. The alphabet treats each pair as two different letters, which is the strongest possible evidence that the distinction mattered to the people who fixed the signs.
What has happened to the series since varies by language and by reading tradition. Arabic keeps it, and keeps it audibly, with a characteristic effect on the vowels next to an emphatic consonant. In the reading traditions of Hebrew the series has been levelled to varying degrees, so the letters remain in the text and are written in full while the distinction they encode is no longer carried in the pronunciation. The Samaritan reading tradition has its own history here, independent of the Tiberian one, and it is one of the traditions linguists consult when they try to reconstruct what the series sounded like earlier.
The general lesson is the one this alphabet keeps teaching. The letters are conservative and the sounds are not. A script that has kept twenty-two signs unchanged for as long as this one has is preserving a phonological system its own readers no longer speak, which is exactly what makes it useful evidence and exactly why it cannot be read as a phonetic transcription.