Cómo filtrar una matriz en un documento Mongodb usando Spring

Como dijiste, elemMatch recuperará solo el primer objeto en una matriz, por lo que debes usar el futuro agregado para lograr tu salida

    MatchOperation match = Aggregation.match(Criteria.where("_id.teacherId").is("1").and("groups.students").in(11));
    UnwindOperation unwind = Aggregation.unwind("groups");
    GroupOperation group = Aggregation.group("_id").push("groups").as("groups").first("points").as("points");
    Aggregation aggregation = Aggregation.newAggregation(unwind, match, group);
    AggregationResults<BasicDBObject> groupResults = mongoTemplate.aggregate(aggregation,
                    CustomGroupsDocument.class, BasicDBObject.class);
    List<BasicDBObject> result = groupResults.getMappedResults();