I am finding that a unique index is not applied to multiple elements of an array in the same document of a collection. They are only applied between documents in a collection.

More details available at: http://groups.google.com/group/mongodb-user/browse_thread/thread/56bf4f84f7cad835

Is this intended behavior? Is there a way around it?

Workaround:
There is a workaround to prevent such duplicates using document validation. You have to create a rule (aka query) that will accept only documents which don't have duplicate values within the same array, and then rely on the unique index to ensure that there are no duplicates across separate documents like before.

Here is an example validator where "a" is an array and within "a" subdocument field "b" value must be unique. This assumes the collection is either empty or already complies with the rule:

> db.coll.createIndex({"a.b":1},{unique:true})
/* validate that incoming documents have as many unique "a.b" values as total "a.b" values */
> db.runCommand({collMod:"coll", validator: {$expr:{$eq:[{$size:"$a.b"},{$size:{$setUnion:"$a.b"}}]}}})
/* test it */
> db.coll.insert({a:[{b:1}]}) /* success */
> db.coll.update({},{ '$push' : { 'a':{b:1}}})
WriteResult({
	"nMatched" : 0,
	"nUpserted" : 0,
	"nModified" : 0,
	"writeError" : {
		"code" : 121,
		"errmsg" : "Document failed validation"
	}
})
> db.coll.insert({a:[{b:5},{b:5,c:11}]})
WriteResult({
	"nInserted" : 0,
	"writeError" : {
		"code" : 121,
		"errmsg" : "Document failed validation"
	}
})

Note that this validator assumes that "a" will always be an array. If "a" is allowed to be a single document then change the validator to

validator:{$or:[{a:{$not:{$type:"array"}}},{$expr:{$eq:[{$size:"$a.b"},{$size:{$setUnion:"$a.b"}}]}}]}})

meaning "a" can be a non-array type OR an array where "b" is not duplicated.