You're not storing the j and i values anywhere, so by the time the buttons have been generated, the values will always be the maximum.

I've quickly cleaned up the code. I added the ability to store the values during creation, and use the accurate values when any button is pressed. I updated the subroutine to accept these values as arguments. Most importantly, I added strict and warnings.

use warnings;
use strict;

use Tk;

my $mw = MainWindow->new(-bg=> '#606060', -borderwidth=> 0);
my $size = 40;
my $y = 0;
my $x = 0;
my $h = 3*$size;

my %frames;

for my $j (0..15) {
    my $x = 0;
    my $w = 3*$size;

    for my $i (0..15) {
        $frames{$j}{$i}{j} = $j;
        $frames{$j}{$i}{i} = $i;
        
        $frames{$j}{$i}{button} = $mw->Button(
            -text => ' ', 
            -bg => "#60C8BC", 
            -fg => "#000000", 
            -borderwidth => 1, 
            -anchor => 'w',  
        );

        $frames{$j}{$i}{button}->bind(
            '<Button-1>' => sub { 
                &ToggleBox($frames{$j}{$i}{j}, $frames{$j}{$i}{i}); 
            } 
        );

        $frames{$j}{$i}{button}->place(
            -y=>$y, 
            -x=>$x, 
            -width=>$w, 
            -height=>$h
        );

        $x = $x + $w;
        $w = $size;
        $x = $x+2 if ($i % 5 == 0);
    }
    $y = $y + $h;
    $h = $size;
    $y = $y+2 if ($j % 5 == 0);
}

MainLoop();

sub ToggleBox {
    my ($j, $i) = @_;
    print "$j, $i\n";
}
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