In Zayd ibn Thabit's account, the Prophet ﷺ stated that punishment was taking place in the graves. The people present did not see the punishment with ordinary sight, but the Prophet ﷺ was given knowledge of it by Allah.
The passing of the graves, the mount's reaction, the identification of those buried there and the news of their condition belong to one connected incident.
The fact that such punishment is ordinarily unseen by people does not establish that it does not exist.