It's possible to get into a hung state in mongos given a sharded cluster with a replica set shard. If the shard primary continues to allow connections but does not respond to other requests, failover will occur and a new primary will be elected normally, but sharded queries via mongos will block and not return.

This failure mode has been observed on EC2.

Can reproduce locally by :
1) Running the script included (sets up a sharded cluster with sharded collection)
2) Running mongo localhost:31000 to connect to the mongos
3) > use foo
4) > db.bar.find().itcount()
5) Stopping all data transfer for connections at the primary via iptables :
sudo /sbin/iptables -A INPUT -i lo -p tcp -m tcp --dport <mongod primary port> -m conntrack --ctstate ESTABLISHED -j DROP
6) (wait for failover)
7) > db.bar.find().itcount()