Nahuatl has two sibilant fricatives, now pronounced something like
[ʃ]. The standard orthography was developed by Spanish colonizers, who wrote
/ʃ/ as x, and
/s/ as c before a front vowel, z elsewhere. (There's also
[t͡ʃ], written ch.)
But since all stages of Spanish definitely had s for
[s], it seems clear that the sound the first transcribers heard definitely wasn't
Do we know what this sound was? There unfortunately weren't trained linguists around transcribing Classical Nahuatl, but the Spanish transcription might be enough to make a good guess.