You need to change the regex that pulls the name out of the text, to something like:

/^\s*(\S+(?:.*\(.*\))?).+\s(\S+)\s*$/
[download]

Okay, here's a slightly updated version that includes that regex, and a minor cleanup:

use strict;
use warnings;

sub readReport {
    my $filename = shift;
    my %hash;
    open (my $file, '<', $filename) or die $!;
    while (<$file>) {
        next unless /^--------/ .. eof;  # Bypass header
        if (my ($name, $score) = /^\s*(\S+(?:.*\(.*\))?).+\s(\S+)\s*$/
+) {
            $hash{$name} = $score;
        }
    }
    return \%hash;
}

my $reportA = readReport('filea');
my $reportB = readReport('fileb');

my %reports = ( fail => [], ignored => [], noCheck => [], pass => [] )
+;
for my $name (sort keys $reportA) {
    my ($a,$b) = ($reportA->{$name}, $reportB->{$name});
    if ($a < 0) {
        push $reports{'noCheck'}, "$name, $a $b" if defined $b;
        push $reports{'ignored'}, "$name, $a 0" unless defined $b;
    } elsif ($a > 50 and $b > 40) {
        push $reports{'pass'}, "$name, $a $b";
    } else {
        push $reports{'fail'}, "$name, $a $b";
    }
}

for my $name (keys %reports) {
    print "\nReport $name\n----------------------\n" ;
    print "$_\n" for @{$reports{$name}};
}
[download]