Per the API docs the /token API call is paged. It appears that the default page size might be 10, so for any system with more tokens than 10 a /usr/bin/privacyidea --url URL -a administrator token list will only list 10 tokens.
I don't see any support in the client lib for paging and I have not reviewed the API docs to see if other calls are paged, so I don't know if the best route is generic support for paging.
If there is no internal momentum on this project I might be able to provide code to solve this issue.