Tried this on 1.2.3:

> db.test.drop();
true
> db.test.save(

{ list: [1, 2] }

);
> db.test.save(

{ list: [1, 3] }

);
> db.test.find( { list:

{ $in: [1], $ne: 3 }

} );

{ "_id" : ObjectId("4b8536ef71f969641118df0b"), "list" : [ 1, 2 ] }

> db.test.ensureIndex(

{ list: 1 }

);
> db.test.find( { list:

{ $in: [1], $ne: 3 }

} );

{ "_id" : ObjectId("4b8536ef71f969641118df0b"), "list" : [ 1, 2 ] } { "_id" : ObjectId("4b8536f371f969641118df0c"), "list" : [ 1, 3 ] }