If you use  if ($line =~ /(\Q$domain\E)/g){ you will only get one $domain per $line.    If you want all $domain per $line then you need to use a while loop:

my %count;
while ( my $line = <RESULT> ) {
    foreach my $domain ( @list ) {
        while ( $line =~ /(\Q$domain\E)/g ) {
            $count{ $1 }++;
            }
        }
    }
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Update: Or better yet, you don't really need capturing parentheses:

my %count;
while ( my $line = <RESULT> ) {
    foreach my $domain ( @list ) {
        while ( $line =~ /\Q$domain\E/g ) {
            $count{ $domain }++;
            }
        }
    }
[download]