In the v2.6 release notes upgrade considerations, for a sharded cluster it states that you should not upgrade mongod instances until you have upgraded the mongos instances.

However, earlier in the Package Upgrades section, the use of apt-get or yum will replace both mongod and mongos binaries at the same time.

This is an issue if the deployment has a mongos running on the same host as a mongod (as a database or config server). In this situation, the workaround is to temporarily use the mongos binary from the v2.6 tgz files. Once the config servers and mongod instances have been upgraded via the package manager, then the mongos can be restarted using the binary from the package manager and the mongos binary from the tgz files will no longer be needed.

I believe this information might be included in the sections to Upgrade Sharded Clusters and Complete Sharded Cluster Upgrade.