It seems from the Srimad-Bhagavatam that Adi-Shankara was simply referring to a variety of spirits:
ḍākinyo yātudhānyaś ca
koṭarā revatī jyeṣṭhā
unmādā ye hy apasmārā
vṛddhā bāla-grahāś ca ye
sarve naśyantu te viṣṇor
English Translation: The evil spirits known as Ḍākinīs, Yātudhānīs and Kuṣmāṇḍas, the evil grahas who take form of children and the evil spirits like Bhūtas, Pretas, Piśācas, Yakṣas, Rākṣasas and Vināyakas, as well as spirits like Koṭarā, Revatī, Jyeṣṭhā, Pūtanā (I'm speculating these to be "Chatur Bhaginyadinis" Adi-Shankara is referring to) and Mātṛkā, are always ready to give trouble to the body, the life air and the senses, causing loss of memory, madness and bad dreams. Like the most experienced evil stars, they all create great disturbances, especially for children, but one can vanquish them simply by uttering Lord Viṣṇu’s name, for when Lord Viṣṇu’s name resounds, all of them become afraid and go away. (Srimad-Bhagavatam 10.6.27-29)
Also, notice the use of the term "vināyakāh" in the same verse. So I think, Adi-Shankara is simply referring to evil spirits when he says "vināyakamātṛgaṇacaturbhaginyādīni" in his commentary on Bhagavad-Gita 9.25.
By the way, Madhusudana Saraswati also includes Yakshas and Rakshasas along with Vinayakas and Matrikas in his commentary of Bhagavad-Gita.