MongoDB Cluster - Can't access member of shard with credentials
When you are using mongoS authentication is done against config servers admin database. When you connect directly to replica set, you are authenticating against replica set's admin database, where you don't have that root user set.

What can you do? Start replica set's (one by one) without --auth parameter (or equivalent config parameter) to maintenance mode, connect that RS with mongo command, create that root user (and other needed users). After that you can restart RS with authentication and you can do login.