Can we improve the API to help customers avoid inserting data with duplicate keys? I am aware that this is technically allowed by the BSON spec, and the server is not enforcing it (we cannot because of backwards compatibility and performance).

The C driver warns about it here. For us on the server, this is a headache. Customers who have this kind of data it is always unintentional and result in query incorrectness, where we have no way of automatic remediation.