When a $geoNear stage is part of a $lookup stage's pipeline, this aggregation will fail with error code 50860. Attached is a script which can be used to reproduce this error by running it from the jstests/aggregation/sources/lookup directory: 

 buildscripts/resmoke.py --suites='aggregation' jstests/aggregation/sources/lookup/lookup_subpipeline_geonear.js 

Part of fixing this test will include making sure this works in the sharded case, and adding test coverage for $geoNear within a $lookup subpipeline. This will include testing that this works with $geoNear using a $$ variable within the query option. For example:

  const pipeline = [
        {
          $lookup: {
              let : {var1: "$x"},
              pipeline: [
                  {$geoNear: {near: [0, 0], distanceField: "distance", spherical: true, query: {_id:"$$var1"},}}, 
              ],
              from: "from",
              as: "c",
          }
        },
    ];

 This does not affect 4.0.