Setting a password with
chpasswd generates a random salt, so users who happen to have the same password would not have identical hashes. In order to have identical hashes this way, you'd have to have a misconfigured system that somehow doesn't save entropy between reboots, and systems that are so completely identical as to repeat the random seed (that can happen with VMs, especially when resuming from snapshots), and for all the passwords to be generated after reading exactly the same number of bytes from
/dev/urandom. This is highly unlikely.
Thus, if you see identical hashes, it means that the hashes were copied. The passwords were deliberately made the same, rather than by coincidentally setting the same password multiple times. Either the administrator directly edited the password database and copying the hashes, or they used something like
chpasswd -e to supply hashes.
The only bad consequence of repeating a password hash is that it makes it apparent that the accounts have the same password. With distinct salts, as is normally the case, it would be impossible to tell that two accounts have the same password except by guessing the password.