Your response alone indicates quite common confusion and misunderstanding and mistaking of many, many things. Transliteration. Transcription. Graphemes. Phonemes. Orthography.
Basically, if you are reading earlier Phoenician texts and you see the S with the diacritic above it (the little crescent) sometimes and sometimes without it, both are pronounced the same. The reason they are written so is because historically, those words were written with those characters because they each were pronounced differently. Also, if you look at later Phoenician texts, some have rid of the diacritic-S altogether since some started writing such that the orthography (spelling) matches the pronunciation.
Don't worry, this is not weird at all. In English, the letter 's' for instance can represent such sounds as [s] and [z]. In 'cats', the 's' sounds like [s], but in 'dogs' it sounds like [z]. Also, one sound may be represented by more than one sound (as in [s] represented by diacritic and non-diacritic S in Phoenician). So in English, the sound [k] comes up as letter 'k' in 'park', but as letter 'c' in 'cat'. Go figure.
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