Hint: Either because he likes people. Or, animals have a good sense of smell.
Schol. A ad Il. 1.50c ex.
“First he [attacked] the mules and the fast dogs”
“Because the god is well-disposed toward human beings, he kills mules, dogs, and the other irrational beasts first, so that, by inducing fear through these [deaths], he might nurture proper reverence in the Greeks.
Or, it is because the mules and dogs have a more powerful perception of smell. For, dogs are really good at tracking beasts because of their sense of smell, and mules, when they are left behind, often rediscover their paths thanks to their sense of smell.”
<οὐρῆας μὲν πρῶτον ἐπῴχετο καὶ κύνας ἀργούς:>
φιλάνθρωπος ὢν ὁ θεὸς πρῶτον τὰς ἡμιόνους καὶ τοὺς κύνας καὶ τὰ ἄλογα ζῷα ἀναιρεῖ, ἵνα διὰ τούτων εἰς δέος ἀγαγὼν τοὺς ῞Ελληνας ἐπὶ τὸ εὐσεβεῖν παρασκευάσῃ. ἢ ὅτι αἱ ἡμίονοι καὶ οἱ κύνες τὴν αἴσθησιν τῆς ὀσφρήσεως ἐνεργεστέραν ἔχουσιν· οἱ μὲν γὰρ κύνες ἀπὸ τῆς ὀσφρήσεως τῶν ἰχνῶν ἐν αἰσθήσει τῶν θηρίων γίνονται, αἱ δὲ ἡμίονοι πολλάκις ἀπολειφθεῖσαι τινων ἀπὸ τῆς ὀσφρήσεως καὶ τὰς ὁδοὺς ἀνευρίσκουσιν.
Additional note: On 1.50, Aristonicus denies the claims by by some rogues that “mules” here is a word for “guards”; the bT scholia make the quasi-scientific claim that these animals are more susceptible to diseases than humans. I like the idea of Apollo trying to teach people a lesson before just murdering them all.