Version 2.6.3 of mongod:
While updating a subdocument rank that is part of contact that is part of user:

This is a MOPED log:
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271020000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>100}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.5676ms
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271030000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>200}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.3991ms
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271040000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>300}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.3387ms
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271050000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>400}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.1929ms
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271060000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>500}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.2453ms
MOPED: 127.0.0.1:27017 UPDATE database=ran_q_test collection=users selector=

{"_id"=>BSON::ObjectId('54a17a0a62656e4271000000'), "contacts._id"=>BSON::ObjectId('54a17a0a62656e4271010000'), "contacts.0.contact_ranks._id"=>BSON::ObjectId('54a17a0a62656e4271070000')}

update={"$set"=>{"contacts.0.contact_ranks.$.value"=>600}} flags=[]
COMMAND database=ran_q_test command={:getlasterror=>1, :w=>1} runtime: 2.2785ms

But seems that instead of updating each document it updates always the first one. The result:
> ranks = db.users.find()[0].contacts[0].contact_ranks
[

{ "_id" : ObjectId("54a179a162656e40ac020000"), "_type" : "ContactRank", "name" : "sexy", "value" : 600 }

,

{ "_id" : ObjectId("54a179a162656e40ac030000"), "_type" : "ContactRank", "name" : "cool" }

,

{ "_id" : ObjectId("54a179a162656e40ac040000"), "_type" : "ContactRank", "name" : "hot" }

,

{ "_id" : ObjectId("54a179a162656e40ac050000"), "_type" : "ContactRank", "name" : "smart" }

,

{ "_id" : ObjectId("54a179a162656e40ac060000"), "_type" : "ContactRank", "name" : "ugly" }

,

{ "_id" : ObjectId("54a179a162656e40ac070000"), "_type" : "ContactRank", "name" : "angry" }

]

In 2.4.12 it works just fine, and the result as it should be:
> ranks = db.users.find()[0].contacts[0].contact_ranks
[

{ "_id" : ObjectId("54a17b2262656e461c020000"), "_type" : "ContactRank", "name" : "sexy", "value" : 100 }

,

{ "_id" : ObjectId("54a17b2262656e461c030000"), "_type" : "ContactRank", "name" : "cool", "value" : 200 }

,

{ "_id" : ObjectId("54a17b2262656e461c040000"), "_type" : "ContactRank", "name" : "hot", "value" : 300 }

,

{ "_id" : ObjectId("54a17b2262656e461c050000"), "_type" : "ContactRank", "name" : "smart", "value" : 400 }

,

{ "_id" : ObjectId("54a17b2362656e461c060000"), "_type" : "ContactRank", "name" : "ugly", "value" : 500 }

,

{ "_id" : ObjectId("54a17b2362656e461c070000"), "_type" : "ContactRank", "name" : "angry", "value" : 600 }

]

I think it is a very serious bug, please reply urgently.
Kind regards, Benjamin Harel.