The most basic problem is that it is impossible (given any realistic i.e. non-Star Trek technology) to map waveforms to IPA letters for an arbitrary language. It is, however, possible for well-enough studied languages, using Google-grade technology, for example you can speak Norwegian or English to Google, it will return the spelling, and you can use that to get an IPA spelling from a phonetic dictionary of the language (except: when there are multiple pronunciations like "to-MAY-toe" and "to-MAW-toe", when you'd need to know how Google handles many-to-1 mappings of pronunciation to spelling).
For the vast majority of languages which are not as well worked out, the problem comes from the fact that mapping between phonetic properties and IPA is many-to-many. For many languages, it is essentially arbitrary whether you will transcribe a given vowel as [i] vs [ɪ], or [ɪ] vs. [e]. Field linguists solve these problems (to the extent that they can be solved – often they cannot) by appeal to myriad poorly- or totally-not understood heuristics, indeed it is well known that the native language as well as fieldwork experience of the fieldworker play a major role in their judgments as to appropriate IPA letter.
IPA letters represent ranges of acoustic and articulatory values (the latter being inaccessible to any speech-recognition program): they are not precise things. The IPA (the association) has not promulgated definitive / authoritative reference recordings or values (especially covering the acceptable range of values, such as F1 and F2 defining [e] vs. [ɪ]). It would also be insufficient to extract such values from Peter Ladefoged's IPA performances, since Ladefoged does not define the IPA standard, and in fact he has made a point of the fact that IPA experts do vary in their pronunciations of "the same thing" (he left us with an illustration of this point for vowel here, and wrote a dissertation on the topic).
Without such standard values, even if you could segment the waveform into candidate segments, and even if you have formant trajectories, that still doesn't tell you which segment you have. A simple illustration (and challenge) is that nobody can give you the defining formant values of [ɨ ə ʌ ø ʊ ɜ ɤ]. You can perhaps find formant values of [ə] is some specific language, but the goal is to find general values.
The above points have focused on the easiest problem to solve: how to map steady-state properties to IPA letters. Segments are rarely "steady" (even within a defined granularity of measurement), so for instance a hallmark of the acoustics of [ɪ ʊ ɛ] in English is that their formant shift over time. This is a language-specific property – [ɪ ʊ ɛ] in Nilotic are reasonably steady-state vowels.
Another issue (which is a bit easier to solve) is that IPA transcriptions can be narrow broad. You could write the distinction between "tab" and "stab" in IPA in many ways: [tæb, stæb], [tʰæb, stæb], [tʰæəb, stæəb], [tʰæəbp, stæəbp]. A narrow transcription hugs the phonetic ground and doesn't care if a transcriptional feature is redundant; a broad transcription gets the essential details of the language. To get a broad transcription, you'd need to first work out the phonological system (how did you do that?).
There is an interplay between "absolutist" judgments in transcription and "rationalist" judgment. What I'm referring to is, on the one hand, a linguist has some standard in mind for "ɪ" (as an absolute thing), but that judgment is modified via exposure to many tokens and a solution to the phonemicization problem (the variation is reasoned away). This kind of reasoning takes many forms. The main form of reasoning that feeds back into transcription decisions is a phonological analysis. If there is a vowel "I" which could reasonably be spelled [ɪ] or [e], but it behaves in the phonology clearly like [i u ɨ] and not like [ɛ ɔ], then you ought to spell "I" as [ɪ]. Fieldworker decisions involve a continuous loop between conscious reasoning about the phonological system and the notion of an absolute acoustic anchor (which I regret to say is a mythical beast).
