So the input is unordered, each line indicates one bean at the location given, and you just want to tally them up and then print them out in grid order? Sounds like:

my %beancounts;
while (<>) {
    my ($x, $y) = split;
    ++$beancounts{$x}{$y};
}
for my $x (sort {$a <=> $b} keys %beancounts) {
    for my $y (sort {$a <=> $b} keys %{$beancounts{$x}}) {
        print "$x $y $beancounts{$x}{$y}\n";
    }
}
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