Hi Julian,
It depends -- if they're live leases, you'll need to revoke them; if not and they're still sticking around they may be hitting some bugs that have since been fixed. As a related note, you really should upgrade to at least 0.6.4 and ideally 0.7.0 as there have been security fixes related to token handling.
Usually if a large number of tokens are being generated it's because processes are logging in to get new tokens constantly instead of re-using tokens they have; or, the token duration is much much longer than the expected user lifetime. You may want to take a look at how Vault is being used to see if you can identify why you have so many tokens from app-id and prevent as many being generated in the future.
Best,
Jeff