Save in a .txt the output that shows me on the screen maintaining the format

You can simplify your code a bit as follows:

<?php
$notas = array(
            'Miguel' => array('Matematicas'=>5, 'Tecnologia'=>5, 'Historia'=>6, 'Ingles'=>8),
            'Ana' => array('Matematicas'=>7, 'Ingles'=>8, 'Lengua'=>6,  'Fisica'=>9, 'Historia'=>5),
            'Luis' => array('Matematicas'=>4, 'Tecnologia'=>4, 'Lengua'=>5,  'Fisica'=>4, 'Historia'=>7),
            'Maria' => array('Matematicas'=>6, 'Tecnologia'=>5, 'Historia'=>6, 'Ingles'=>4),
            'Antonio' => array('Matematicas'=>4, 'Tecnologia'=>5, 'Lengua'=>5,  'Fisica'=>4, 'Historia'=>4, 'Ingles'=>6),
            'Raul' => array('Matematicas'=>4, 'Tecnologia'=>5, 'Lengua'=>7,  'Fisica'=>5, 'Historia'=>6, 'Ingles'=>8)
);

ksort($notas);

$ficheroSalida = fopen("salida.txt","a");

echo "<table border='1'><tr><th>Nombre del alumno</th><th>Nota Media</th><th>Aprobados</th><th>Suspensos</th></tr>";

foreach($notas as $nombre => $notasAlumno) {
    $totalNotas = count($notasAlumno);
    $aprobados = count(array_filter($notasAlumno, function($nota) { if($nota >= 5) return $nota; }, 0));
    $suspensos = $totalNotas - $aprobados;
    $notaMedia = number_format(array_sum($notasAlumno) / $totalNotas, 2);

    $linea = implode(',', array($nombre, $notaMedia, $aprobados, $suspensos)) . PHP_EOL;

    fwrite($ficheroSalida, $linea);

    echo "<tr><td>".$nombre."</td><td>".$notaMedia."</td><td>".$aprobados."</td><td>".$suspensos."</td></tr>";
}

echo "</table>";

fclose($ficheroSalida);
?>

In your code, for each grade you set the array $arrayFinal (Average, approved, failed), you would have to do this when you finish processing the grades of each student (that is, outside the most nested foreach, where you echo the row for table).

Also directly there you could write the line to the file (instead of saving the data in the $arrayFinal array), and not use two foreach afterwards to do it.

After analyzing the comments on your post, I suspect that the problem is in the following assignment $arrayFinal[$nombre]=$notaMedia; , since you are only assigning $notaMediaeach user's assignment, when what (I think) you want to do is store all their values. Thus, it is as easy as adding them keysto the same array:

 $arrayFinal[$nombre]['Media'] = $notaMedia;
 $arrayFinal[$nombre]['aprobados'] = $aprobados;
 $arrayFinal[$nombre]['suspensos'] = $suspensos;

and then iterate to print it all to the TXT file. I recommend you uncomment the line //print_r ($arrayFinal);so that you can see the contents of the array on the screen beforehand and thus be able to self-debug the logic errors in your code.

You may find it helpful to use more concrete variable names than

$arrayFinal as $clave=>$valor

Maybe that way you would see how within you you $arrayFinalare saving the $nombrestudent's and his $notaMediaand not the rest of the values ​​that you also want.

UPDATE :

Modify your code so you can see more clearly where the error is. Instead of writing directly to the file with fwritetry creating a type variable $lineathat contains the line of text you want to write to the file. Use echoor print_rin your code for each iteration of your loops if necessary.

The code you are looking for would look something like this:

foreach($arrayFinal as $nombres=>$array)
{   
    $linea = $nombreAlumno . ",";
    foreach ($array as $indice => $valor)
    { 
      $linea .= $valor . ",";
    }
    $linea = substr($linea, 0, -1); //le quitamos la última coma
    print_r($linea); //compruebo que la linea tiene los datos que quiero
    //imprimo $linea en mi fichero txt
}