Why did Sai Baba instruct his followers to be hostile and avoid certain people, even telling them to shoo away dogs and pigs?

This appears to be a misunderstanding of Sai Baba's guidance. The text from Chapter 3 presents two distinct teachings. Baba advises that one should move aside from and not even stay in the shadow of a person who has "abandoned religious conduct" and whose character is fallen, considering them dangerous to one's spiritual path. Conversely, regarding animals and other beings, Baba's instruction was the complete opposite. He explicitly said, "Do not shoo away (had-had) anyone, be it a dog, pig, or fly," teaching that no one who comes to us should be driven away, as there is a connection with everyone.