It seems after sorting a cursor that is querying a sharded collection, the documents that the cursor returns are missing $-prefixed fields. Repro of the bug, provided by max.hirschhorn@mongodb.com:

(function() {
"use strict";

const document = ({_id: 5, $set: {$inc: {x: 5}}});
assert.commandWorked(db.mycoll.insert(document));
assert.eq([document], db.mycoll.find().hint({$natural: 1}).toArray());
assert.eq([document], db.mycoll.find().hint({_id: 1}).toArray());
assert.eq([document], db.mycoll.find().sort({_id: 1}).toArray());
})();

will fail on the sort() call if run in the sharded_collections_jscore_passthrough suite.

This bug happens on 5.0, 6.0, and master. We should also investigate if this applies to dot prefixed fields as well.