Even though many languages are still written in Devanagari, they have a problem of schwa deletion. But that problem doesn't exist in Sanskrit. I know that almost all languages have phonetic inconsistencies, does any such problem exist in Sanskrit as well?
What people usually mean by a language being "phonetic" is that from the writing, you can tell exactly how the written text is supposed to be pronounced, if you know how to interpret the letters correctly. This is the case with Sanskrit, at least as far as we can determine. That is, for any spelling of a text, there are no lexical ideosyncracies in how it is to be read. There is one area of uncertainty, namely accent in Classical Sanskrit (not Vedic), that we don't know where the accent is in the later language, and there is no written indication.
I mostly agree with the other answer by user6726. However, I would like to point out a subtle variation in the pronunciation of the letter अ in Sanksrit with the region it is spoken. The speakers from Indian Eastern Ghats i.e. Bengal and Odisha speak it in a way closer to oʊ (as in boat) and ɔ: (as in paw) respectively, unlike those in Northern Plains who speak it as ə (as in about). Although I was taught that way in an English-medium school in India, the latter may not necessarily be the standard way of speaking since I have seen learned priests in different regions recite the rituals in varying tones.
Other than this, I cannot find any instance where a letter can have two sounds in Sanskrit.