It seems that there is a permission issue on db.system.users.getIndexes() in 3.0. In 2.6, this seems to be working fine. Following are the steps that I used to replicate this issue:

1. Install MongoDB 2.4 (Since users were stored in <database>.system.users collection in 2.4).
2. Create user with readWrite and dbOwner role.

   db.addUser( { user: "user", pwd: "user", roles: ["readWrite","dbOwner"] } )
   ankit(mongod-2.4.14) test> db.system.users.find()
   {
     "_id": ObjectId("55fb9dc4ab757ec03e77562d"),
     "user": "user",
     "pwd": "fa26a506aa0f786a447bbd6d1caaa8b5",
     "roles": [
       "readWrite",
       "dbOwner"
     ]
   }
   

3. Start MongoDB and execute following queries:

   ankit:log-11213 ankit$ mongo
   MongoDB shell version: 2.4.14
   connecting to: test
   Mongo-Hacker 0.0.8
   > db.auth("user","user")
   1
   > show collections
   system.indexes → 0.000MB / 0.004MB
   system.users   →   NaNMB /   NaNMB
   > db.system.users.getIndexes()
   [
     {
       "v": 1,
       "name": "_id_",
       "key": {
         "_id": 1
       },
       "ns": "test.system.users"
     },
     {
       "v": 1,
       "name": "user_1_userSource_1",
       "key": {
         "user": 1,
         "userSource": 1
       },
       "unique": true,
       "ns": "test.system.users"
     }
   ]
   

4. Upgrade to 2.6 (Note that it requires authorization schema upgrade). Users will be copied to admin.system.users collection. But <database.system.users> collection still remains in the database in question.
5. Connect via mongo client and execute following query:

   connecting to: test
   Mongo-Hacker 0.0.8
   > db.auth("user","user")
   1
   > show collections
   system.indexes → 0.000MB / 0.004MB
   system.users   →   NaNMB /   NaNMB
   > db.system.users.getIndexes()
   [
     {
       "v": 1,
       "name": "_id_",
       "key": {
         "_id": 1
       },
       "ns": "test.system.users"
     },
     {
       "v": 1,
       "name": "user_1_userSource_1",
       "key": {
         "user": 1,
         "userSource": 1
       },
       "unique": true,
       "ns": "test.system.users"
     }
   ]
   

6. Upgrade to 3.0.5, connect via mongo and execute following command:

   ankit:log-11213 ankit$ mongo
   MongoDB shell version: 3.0.5
   connecting to: test
   > db.auth("user","user")
   1
   > db.system.users.getIndexes()
   2015-09-18T11:01:15.116+0530 E QUERY    Error: listIndexes failed: {
     "ok": 0,
     "errmsg": "not authorized on test to execute command { listIndexes: \"system.users\" }",
     "code": 13
   }
       at Error (<anonymous>)
       at DBCollection._getIndexesCommand (src/mongo/shell/collection.js:1019:15)
       at DBCollection.getIndexes (src/mongo/shell/collection.js:1026:20)
       at (shell):1:17 at src/mongo/shell/collection.js:1019
   

Notice the permission issue coming in 3.0.5 while it was working fine in 2.6.