How about this?

#!/usr/bin/env perl 

use strict;
use warnings;

my $data = "test1 ERROR1 ERROR1:TYPE1
test2 ERROR1 ERROR1:TYPE2
test3 ERROR2 ERROR2:TYPE1
test4 ERROR1 ERROR1:TYPE1
test5 ERROR2 ERROR2:TYPE1
test6 ERROR2 ERROR2:TYPE2
";

my @data = map [ split /\s+/, $_ ], split "\n", $data;

my %nested;
for (@data) {
    my ($file, $error, $type) = @$_;
    push @{ $nested{$error}{$type} }, $file;
}

for my $error (sort keys %nested) {
    print "\n##", $error, $/;
    for my $type (sort keys %{ $nested{$error} }) {
        print '#', $type, $/;
        print join( ', ', @{ $nested{$error}{$type} } ), $/;
    }
}

__DATA__
outputs:
## ERROR1
# ERROR1:TYPE1
test1, test4
# ERROR1:TYPE2
test2

## ERROR2
# ERROR2:TYPE1
test3, test5
# ERROR2:TYPE2
test6
[download]

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)