Mixe-Zoquean languages seem to be "almost" languages, whether they count as twelve or less is going to depend on where you draw the line.
Ayutla/South Highlands Mixe has 12 *native* consonants /p t ts k ʔ s ʂ h m n j w/ (with the interesting feature that /ʂ/ is the basic sibilant, /s/ is highly limited). There are, however, a bunch of loaned consonants from Spanish, plus /l/, which is mostly in loans but also the word /kulʌk/ "turkey," possibly onomatopoeic, and /kipljɤ:/ "stump" from /kipj/ "stick" plus an unidentifiable morpheme.
Sierra Popoluca has 12 /p t ts k ʔ s h m n ŋ w j/, plus a phoneme that surfaces as vowel length before consonants, vowel length and [h] word-finally, and null before the completive+"already" portmanteau [-wɨm]. Again, however, there are a bunch of Spanish loan consonants. There's also a palatalized set [tʲ dʲ ʃ tʃ ɲ], with almost all of them occurring as allophones of /t s ts n/ next to /j i/ (or before a palatalized consonant before /i/), but minorly phonemic due to loans from Spanish, loans from Spanish that fail to palatalize in the appropriate environment, rare word-final instances (whereas in Ayutla Mixe they are clearly clusters of Cj even finally), and they appear in sound symbolic expressions. Sound symbolism also has /l r/. And there's a small handful (less than a dozen, from what I can tell) of voiced sounds that appear without the following /ʔ/ that normally triggers voicing, such as the suffix /-gak/ "another/again" and /dʲa/ "no."
San Miguel Chimalapa Zoque has 11 /p t ts k ʔ ʃ h m n w~ŋ j/ (the grammar lists 12, but [w] appears in onsets and [ŋ] in codas, so I see no reason to treat them as distinct phonemes). In addition to a bunch of Spanish loan consonants, are normally found as allophones of voiceless stops but they show up word-initially in some 1st person pronouns, deictics, and a few other function words regardless of context. /s f l r/ appear in Spanish loans, a tiny number of words of unknown origin, and in sound symbolic expressions.