make the average with 2 values from Json with AngularJS

Your code has a few issues that I will try to make it clear for you. Let's start with the HTML.

ng-if="stat.mediaGoals()" will ever be matched, because the object stat does not have a mediaGoals function, and even if it has it, your mediaGoals function returns nothing, undefined to be more specific. Also, mediaGoals in this case, is a real performance killer.

My recommendation is to parse/convert the JSON in the service that loads it, converting the content into something more easy to handle in the HTML.

As I don't know the code that loads the JSON, I will adapt an illustrative example of your code and hope it helps.

Suppose we are using $http to load the JSON from an API

$http(requestConfig)
    .then(function(response){
        var players = [];
        for (var i = 0; i < response.data.length; i++) {
            var item = response.data[i];
            var player = {
                player: item.player,
                stats: { media: 0 }
            };
            var tmp_goals = 0;
            var tmp_mins = 0;

            for (var x=0; x < item.stats.length; x++) {
                var stat = item.stats[x];

                player.stats[stat.name] = stat.value;

                switch(stat.name) {
                    case 'goals':
                        tmp_goals = stat.value;
                    break;
                    case 'mins_played':
                        tmp_mins = stat.value;
                    break;
                }
            }

            if (tmp_mins > 0) {
                player.stats.media = tmp_goals/tmp_mins;
            }

            players.push(player);
        }

        return players;
    });

Now, every time we get a single item from this list, it will look like this:

{
    player: {
      info: ...same from anwser
    },
    stats: {
        appearances: 80,
        backward_pass: 308,
        draws: 23,
        fwd_pass: 1533,
        goal_assist: 2,
        goals: 5,
        losses: 20,
        media: 0.0007191140514885661,
        mins_played: 6953,
        wins: 48
    }
}

Note that I did not include some info for brevity. But now, when we set the value to $scope.Jugador with one item from the parsed/converted list, the HTML will become much simpler, not need of ngRepeat or ngIf.

<div class="stadistics">
    <div class="cont-desc-player">
        <div class="desc-player separador">
           <span class="txt-estadistics">Appearances</span>
           <span class="num-estadistics">{{Jugador.stats.appearances}}</span>
        </div>
        <div class="desc-player separador">
            <span class="txt-estadistics">Goals</span>
            <span class="num-estadistics">{{Jugador.stats.goals}}</span>
        </div>
        <div class="desc-player separador">
            <span class="txt-estadistics">Assists</span>
            <span class="num-estadistics">{{Jugador.stats.goal_assist}}</span>
        </div>
        <div class="desc-player separador">
            <span class="txt-estadistics">Goals per match</span>
            <span class="num-estadistics">{{Jugador.stats.media}}</span>
        </div>
    </div>
</div>

Or probably you want to keep the ngIf and only show the info if the value is greater than 0

<div class="desc-player separador" data-ng-if="Jugador.stats.media > 0">
    <span class="txt-estadistics">Goals per match</span>
    <span class="num-estadistics">{{Jugador.stats.media}}</span>
</div>

It is all up to you from now on, hope it help.

EDIT:
If you want to continue with your approach on mediaGoals function, then you need to invoke it in your controller before you set the value to Jugador, so, it needs some changes.

$scope.Jugador = mediaGoals($scope.players[0]);


function mediaGoals(jugador) {
    var tmp_goals = 0;
    var tmp_mins = 0;
    for (var i = 0; i < jugador.stats.length; i++) {
        switch(jugador.stats[i].name) {
            case 'goals':
              tmp_goals = jugador.stats[i].value;
            break;
            case 'mins_played':
              tmp_mins = jugador.stats[i].value;
            break;
        }

    }

    jugador.stats.push({ name: 'media', value: tmp_mins > 0 ? tmp_goals/tmp_mins : 0 });

    return jugador;
}

Adjust $scope.players[0] to your needs.

Now, your HTML can change to this

<div class="desc-player separador" ng-if="stat.name == 'media'">
    <span class="txt-estadistics">Goals per match</span>
    <span class="num-estadistics">{{stat.value}}</span>
</div>