This is definitely an edge case, but probably should work (referenced here: http://groups.google.com/group/mongodb-user/browse_thread/thread/32511a51caad9085). Here's how to reproduce:

> db.a.save({a: {spec: [{ info: [

{key: "author", value: "poe"}

]} ]}})
> db.a.find()
{ "_id" : ObjectId("4e5d23ba339dc0b7074165f6"), "a" : { "spec" : [ { "info" : [

{ "key" : "author", "value" : "poe" }

] } ] } }

> db.a.find(

{"a.spec.0.info.0.key": "author", "a.spec.0.info.0.value": "poe"}

)
{ "_id" : ObjectId("4e5d23ba339dc0b7074165f6"), "a" : { "spec" : [ { "info" : [

{ "key" : "author", "value" : "poe" }

] } ] } }

So far so good. Now add an index:
> db.a.ensureIndex(

{"a.spec.0.info.0.key": 1, "a.spec.0.info.0.value": 1}

)

> db.a.find(

{"a.spec.0.info.0.key": "author", "a.spec.0.info.0.value": "poe"}

)
Returns nothing!