Atomic applyOps is no longer supported. A change made to jstests around Mongomirror is linked here: https://github.com/10gen/mongo/blob/master/jstests/core/apply_ops_missing_field.js#L29

Description of Linked Ticket

All the 3.6 uses of applyOps are only on the same mongod. The use on config servers has been replaced with doTxn and will eventually be replaced with multi-statement transactions, so we should be able to remove atomic applyOps in 4.0.