Today, applyOps doesn’t work with sharded clusters. And, because replica set endpoint acts on top of a 1-shard cluster, and we don’t have parity with MongoS for applyOps (internal command), the expected behavior is the same as applying applyOps as a direct connection to a shard.

Until SERVER-84342 is completed, the agreed solution has been to disable applyOps testing with replica set endpoint.