In the page :
http://docs.mongodb.org/manual/reference/method/db.collection.createIndex/#db.collection.createIndex

We can read the following sentence:

Use db.collection.createIndex() rather than db.collection.createIndex() to create new indexes.

I do not want to provide any fix, since I am not sure what's this message is about.
Source:

https://github.com/mongodb/docs/blob/0198b5c74a740a9fd85ecc5bd8b3ac4aefde7d2b/source/reference/method/db.collection.createIndex.txt#L139-L140