The aggregation used to find sharded indexes that aren't on all shards with chunks (added by SERVER-44916 and modified by SERVER-46084) only considers a subset of the possible properties in an index specification when comparing them to work around the inability to cleanly compare BSON objects ignoring field order in aggregation. After SERVER-29425 adds official support for ordering an array, the pipeline should be updated to compare entire index specifications with unordered object comparisons using $objToArray, the new sort expression, and then $arrayToObj.