Latin orthography seems to have been relatively phonemic. In other words, if long vowels are marked somehow (macrons or apices), there seems to be a straightforward mapping between letters and phonemes in the language.
Are there any real exceptions to this: Classical-era phonemic distinctions that aren't represented in spelling?
(I know long vowels are often left unmarked, so that alium and ālium look the same. But for the purposes of this question, assume vowel length is marked consistently and reliably.)