1) Arara (Arára do Pará) has a voicing distinction for plosives; the voiced ones are missing in the inventories. While they transparently derive from unvoiced ones, and while there is still variation (i.e., an ongoing change), Alves (2010: 12) gives minimal pairs for bilabial, alveolar, and velar plosives.
2) Waimirí-Atroarí has a voiceless velar plosive /k/, which is missing. The saphon inventory seems to be based on a footnote in Bruno (2003a: 84), which briefly lists the phoneme inventory, but is missing /k/. Examples of /k/ abound in the examples in the rest of Bruno (2003a), however. It is also listed as part of the seventeen consonant phonemes in Bruno (2003b: 32).
3) The inventory of Suyá is based on Guedes (1993). While dos Santos (1997) does not focus on the phonology, she does make some corrections to Guedes’ inventory:
a) Guedes’ /ɣ/ is better represented as /h/, with most of the allophones in Guedes (1993: 56) being [h] or [χ], and with some instances of cluster /hr/ and /hw/ being heard as /ɣ/ by Guedes (dos Santos 1997: 14).
b) There is a vowel missing in Guedes (1993): /ɜ/, in contrast with /ə/, analogous to /e/ vs /ɛ/ and /o/ vs /ɔ/. (The vowel is written as /ʌ/ by dos Santos [1997: 24], but it is clearly a central mid-open vowel, as also found in other Northern Jê languages).
c) Guedes (1993: 50-51) gives [j] as a free variant of a phoneme /d͡ʒ/, and analyzes /ɲ/ as another phoneme (1993: 53). Dos Santos (1997: 23) subsumes all of these in a single phoneme /j/, where [j] is in free variation with [d͡ʒ], and [ɲ] occurs in nasal contexts. (Guedes 1993:50 also gives [ɲd͡ʒ] as another free variant). So /d͡ʒ/ and /ɲ/ should be deleted, and /j/ should be added, which has the allophone [ɲ] in nasal contexts, and [ɲd͡ʒ] ~ [d͡ʒ] ~ [j] in oral ones.
4) Djeoromitxí has a vowel /ʉ/, which is in contrast with /u/ (Ribeiro & van den Voort 2010: 531), as evidenced by minimal pairs such as /ku/ ‘tree’ vs /kʉ/ ‘hole’ (Pires 1992: 40).
Todo: fix.
Many thanks to @fmatter for pointing these out:
1) Arara (Arára do Pará) has a voicing distinction for plosives; the voiced ones are missing in the inventories. While they transparently derive from unvoiced ones, and while there is still variation (i.e., an ongoing change), Alves (2010: 12) gives minimal pairs for bilabial, alveolar, and velar plosives.
glottocode: para1310, phoible: https://phoible.org/inventories/view/1864 saphon: http://linguistics.berkeley.edu/~saphon/en/inv/AraraPara.html
2) Waimirí-Atroarí has a voiceless velar plosive /k/, which is missing. The saphon inventory seems to be based on a footnote in Bruno (2003a: 84), which briefly lists the phoneme inventory, but is missing /k/. Examples of /k/ abound in the examples in the rest of Bruno (2003a), however. It is also listed as part of the seventeen consonant phonemes in Bruno (2003b: 32).
glottocode: waim1253 phoible: https://phoible.org/inventories/view/1885 saphon: http://linguistics.berkeley.edu/~saphon/en/inv/WaimiriA.html
3) The inventory of Suyá is based on Guedes (1993). While dos Santos (1997) does not focus on the phonology, she does make some corrections to Guedes’ inventory:
a) Guedes’ /ɣ/ is better represented as /h/, with most of the allophones in Guedes (1993: 56) being [h] or [χ], and with some instances of cluster /hr/ and /hw/ being heard as /ɣ/ by Guedes (dos Santos 1997: 14).
b) There is a vowel missing in Guedes (1993): /ɜ/, in contrast with /ə/, analogous to /e/ vs /ɛ/ and /o/ vs /ɔ/. (The vowel is written as /ʌ/ by dos Santos [1997: 24], but it is clearly a central mid-open vowel, as also found in other Northern Jê languages).
c) Guedes (1993: 50-51) gives [j] as a free variant of a phoneme /d͡ʒ/, and analyzes /ɲ/ as another phoneme (1993: 53). Dos Santos (1997: 23) subsumes all of these in a single phoneme /j/, where [j] is in free variation with [d͡ʒ], and [ɲ] occurs in nasal contexts. (Guedes 1993:50 also gives [ɲd͡ʒ] as another free variant). So /d͡ʒ/ and /ɲ/ should be deleted, and /j/ should be added, which has the allophone [ɲ] in nasal contexts, and [ɲd͡ʒ] ~ [d͡ʒ] ~ [j] in oral ones.
glottocode: suya1243 phoible: https://phoible.org/inventories/view/1973#tipa saphon: http://linguistics.berkeley.edu/~saphon/en/inv/Suya.html
4) Djeoromitxí has a vowel /ʉ/, which is in contrast with /u/ (Ribeiro & van den Voort 2010: 531), as evidenced by minimal pairs such as /ku/ ‘tree’ vs /kʉ/ ‘hole’ (Pires 1992: 40).
glottocode: djeo1235 phoible: https://phoible.org/inventories/view/1960#tipa saphon: http://linguistics.berkeley.edu/~saphon/en/inv/Jabuti.html