Problems creating or updating records from array

When you pass the query variable to do the find in Note, you only have to pass the student_id and the_id_id, because as you have declared, you are waiting to find the document with all the parameters:

query.delegacion = data.delegacion;
query.disciplina = data.disciplina;
query.periodo    = data.periodo;
query.nivel      = data.nivel;
query.anio       = data.anio;

I also suggest you pass to a function the part of creating Note, you pass the parameters of the query only student_id and master_id, nro_note and use a callback:

function agregarNota(query, nro_nota, callback) {
        Nota.find(query)
            .exec(function(err, result) {
                if (err) res.send(err);
                if (result.data) {
                    result.nota = nro_nota;
                    result.save(function(err, doc) { });
                    return callback(true)
                } else {
                    var notas = new Nota();
                    notas.delegacion = data.delegacion;
                    notas.disciplina = data.disciplina;
                    notas.periodo  = data.periodo;
                    notas.nivel    = data.nivel;
                    notas.anio     = data.anio;
                    notas.alumno   = id_alumno;
                    notas.materia  = id_materia;
                    notas.fecha    = req.body.fecha;
                    notas.nota     = nro_nota;
                    notas.recupera = false;

                    notas.save(function(err, doc) { });
                    return callback(true);
                }
            });
    }

I think the problem is in the query variable, so you pass your query to mongodb:

{ delegacion: 'delegacion',
  disciplina: 'disc',
  periodo: 'periodo',
  nivel: 1,
  anio: 2017,
  alumno: '57e4393fcc6f162d3166925e',
  materia: '58ae61d38f89a5574c28bdd4' }

If you prefer to leave the search function inside the for loop, the variable nro_nota can change, take it into account.

Use ES6 code as much as you can so you can take advantage of the many novelties offered by the most modern version of the language. First, never use var as a control variable if you are going to reference it in a callback simply because it will not work as you think.

JavaScript is an asynchronous language, callbacks are not executed sequentially in the code, if not in parallel, making it quite possible that when the callback is executed the loop has already ended and always references the last record each time. You can read about closures to have a more detailed idea about it.

Another tip is that always modularize your code , always, no matter how small. Identify responsibilities, delégate them, divide your application into layers , each with a single responsibility. For example, all logic with database should be isolated from the rest and serve only as a service for when you need to bring data from the database.

Your code, it looks like this using ES6:

Router handler

let notasRepository = new NotasRepository();

for (let alumno in data.notas) {
  for (let materia in data.notas[alumno]) {
    let nota = data.notas[alumno][materia];

    notasRepository.createOrUpdate({
      delegacion: data.delegacion,
      disciplina: data.disciplina,
      periodo: data.periodo,
      nivel: data.nivel,
      anio: data.anio,
      fecha: req.body.fecha,
      materia,
      alumno,
      nota
    })
    .then(doc => {
      // tienes disponible cada documento creado o actualizado
    });
  }
}

NotasRepository

export default class NotasRepository {

  updateOrCreate (params) {
    let where = (
      ({ delegacion, disciplina, periodo, nivel, anio, alumno, materia })) =>
      ({ delegacion, disciplina, periodo, nivel, anio, alumno, materia })
    )(params);

    return new Promise((resolve) => {
      Nota
        .find(query)
        .then(doc => {
          if (doc) {
            doc.nota = params.nota;
            doc.save().then(() => {
              resolve(doc);
            });
          } else {
            where.materia = params.materia;
            where.alumno = params.alumno;
            where.fecha = params.fecha;
            where.nota = params.nota;
            where.recupera = false;

            Nota.create(where).then((doc) => {
              resolve(doc);
            });
          }
        });
    });
  }
}