The recommended process for doing a sharded cluster version upgrade is:

• Upgrade mongos (with --upgrade)
• Upgrade shards
• Upgrade config servers

However, when running this for a 2.4 to 2.5 version upgrade, the following error is thrown when a client (e.g. a mongo process) attempts to run the authSchemaUpgradeStep command on the admin database.

{
	"ok" : 0,
	"errmsg" : "SyncClusterConnection::update prepare failed:  localhost.mongodb.com:29001:10276 DBClientBase::findN: transport error: localhost.mongodb.com:29001 ns: admin.$cmd query: { resetError: 1 } localhost.mongodb.com:29002:10276 DBClientBase::findN: transport error: localhost.mongodb.com:29002 ns: admin.$cmd query: { resetError: 1 }",
	"code" : 8005
}

However if the order is changed a bit:

• Upgrade shards
• Upgrade config servers
• Upgrade mongos (with --upgrade)

There are no issues upgrading in this order.