G'day Dimitri,

The fact that accessing $config->{item} with a hash key worked (i.e. $config->{item}{"bla"}), while accessing it with an array index gave an error (i.e. $config->{item}[$i]), should have provided a huge clue as to what was going on. Regardless, in situations where you are encountering these sorts of difficulties, it's quite useful to look at the data structure that XML::Simple is generating (e.g. with Data::Dumper):

$ perl -Mstrict -Mwarnings -E '
    use Data::Dumper;
    use XML::Simple qw{:strict};

    my $xml = <<EOX;
<?xml version="1.0" encoding="UTF-8"?>
<config>
    <item>
        <id>0</id>
        <filename>AMEX</filename>
        <destination_dir>test</destination_dir>
    </item>
    <item>
        <id>1</id>
        <filename>bla</filename>
        <destination_dir>test1</destination_dir>
    </item>
    <item>
        <id>2</id>
        <filename>alb</filename>
        <destination_dir>test2</destination_dir>
    </item> 
</config>
EOX
    
    my $config = XMLin($xml => KeyAttr => {item=>"filename"}, ForceArr
+ay => ["item"]);
    print Dumper $config;
'
$VAR1 = {
          'item' => {
                    'alb' => {
                             'id' => '2',
                             'destination_dir' => 'test2'
                           },
                    'AMEX' => {
                              'destination_dir' => 'test',
                              'id' => '0'
                            },
                    'bla' => {
                             'id' => '1',
                             'destination_dir' => 'test1'
                           }
                  }
        };
[download]

Armed with that information, it should now be easy to extract the data you want:

$ perl -Mstrict -Mwarnings -E '
    use XML::Simple qw{:strict};

    my $xml = <<EOX;
<?xml version="1.0" encoding="UTF-8"?>
<config>
    <item>
        <id>0</id>
        <filename>AMEX</filename>
        <destination_dir>test</destination_dir>
    </item>
    <item>
        <id>1</id>
        <filename>bla</filename>
        <destination_dir>test1</destination_dir>
    </item>
    <item>
        <id>2</id>
        <filename>alb</filename>
        <destination_dir>test2</destination_dir>
    </item> 
</config>
EOX
    
    my $config = XMLin($xml => KeyAttr => {item=>"filename"}, ForceArr
+ay => ["item"]);

    say "*** bla destination ***";
    say $config->{item}{bla}{destination_dir};

    say "*** all destinations ***";
    for (keys %{$config->{item}}) {
        say "$_: ", $config->{item}{$_}{destination_dir};
    }
'
*** bla destination ***
test1
*** all destinations ***
alb: test2
AMEX: test
bla: test1
[download]

If you need to change the options to XMLin, continue to use Data::Dumper (or your preferred equivalent) to see the effects of those option changes.