Por causa do funcionamento deste programa. Citando man ssh-copy-id
:
ssh-copy-id is a script that uses ssh(1) to log into a remote machine (presumably using a login password, so password authentication should be enabled, unless you've done some clever use of multiple identities). It assembles a list of one or more finger‐ prints (as described below) and tries to log in with each key, to see if any of them are already installed (of course, if you are not using ssh-agent(1) this may result in you being repeatedly prompted for pass-phrases). It then assembles a list of those that failed to log in, and using ssh, enables logins with those keys on the remote server.
Eu concordaria que isso pode ser inteligente demais às vezes, mas este não é o lugar para perguntar "por que", já que não somos os desenvolvedores.