Suspiciously many entries are listed as having a cognate in only one Berber language (eg earth, hide, skin, run away); given the general closeness of different Berber varieties, you would expect valid proto-Berber terms to be reflected in more than one place. However, these could always be right. Other issues are more serious.
In several cases, a single proto-Berber root is split across several AA ones, due to mistaken sound correspondences. For example:
- Proto-Berber *i-qăs "bone, (fruit) pit" is split between PAA *ʔayš/ʔawš- "ripened grain, corn" with Zenaga iʔssi (quoted without the glottal stop) "os; grain, graine, baie; comprimé, pilule, cachet, pastille; perle" (Taine-Cheikh), and *ḳ(ʷ)as "bone", with all other reflexes of *iqăs, even though Berber γ (<*q) commonly corresponds to Zenaga ʔ.
- Proto-Berber *ta-Hăli (> *ti-Həli) "sheep" is split between pAA *ʔayl "ram" and *bawil "ram", although Ghadames-Awjila v corresponds regularly to Tuareg h and other Berber Ø. (A couple of forms, like Figuig tili mistakenly glossed as "ram", have even somehow found their way into a third etymon, "proto-Berber" *laH!) The issue is alluded to in a cryptic comment under the Berber section of PAA *waʔil "wild goat/ram; antelope": "Pr. H No. 220 (and Kössm. 193): Ghdm., Audj. Hgr etc. te-hele < *tiHeli, which, on the contrary, is to be connected with *ʔayl- 'ram' 3061 (together with Brb. forms of the t-ili type), as *ʔ > h in Hgr, while *ʕ > Hgr 0".
Most reflexes of pan-Berber ikərri / akrar "ram" are assigned to PAA *kar(w)- "ram, goat; lamb; kid". (The Semitic parallels listed for this word are rather interesting.) But Zenaga ǝgrǝrh, pl. gurănh 'bélier' (Nic. 156), on its own, is given a supposed proto-Berber form *gur- "ram", corresponding to an AA form *(ʔa-)gʷar "kind of antelope; ram; goat". In fact, however, there is a common correspondence of Zenaga g followed by a sonorant to proto-Berber k (eg ägärgur "chest" = Siwi ikərkər, əməgyih "dine" = Kabyle iməkli etc), and this word is obviously related to the other Berber forms.
- Most reflexes of Proto-Berber *a-lăqŭm "camel" are under PAA *ʕalVḳ/g- ˜ *lVḳ/gum- ˜ *ḳalVm- "camel"; but the Zenaga one äyiʔm, with regular *l > y (in his source's transcription ǯ) and common *γ > ʔ as seen previously, ends up as PAA *gam-al- (?).
- Under PAA *kʷay(-t)- "hen; partridge; dove; chick" is listed a "proto-Berber" form *i-kaHi; but the Ahaggar form listed corresponds regularly to Niger Tuareg tekažit, Mali Tuareg tekazzit, Awjila təkažit "hen" (see Kossmann 2005:60), and as such is unrelated to the Ayr and Tawllemmet forms takəyya quoted.
Interestingly, most of the problem cases I've noticed in this quick skim are related to agricultural terminology. I wonder if that has anything to do with the particular interest of such terms for archeologists motivating a more intense search for cognates.