f = db.jstests_indexg;
f.drop();
f.save({list: [1, 2]});
f.save({list: [1, 3]});

doit = function() {
    assert.eq(1, f.count({list: {$in: [1], $ne: 3}}));
    assert.eq(1, f.count({list: {$in: [1], $not: {$in: [3]}}}));
};
doit();
f.ensureIndex({list: 1});
doit();