Here's my guess:

Your file has Windows newlines (cr/lf), which your editor/viewer can deal with and shows it correctly. Then you add unix newlines (lf) on the lines you edit. Now there are mixed cr/lf and lf newlines, which confuses the editor and it shows the cr characters.

If I'm correct, then I recommend either preprocess the file with the dos2unix tool or address this in the perl script itself

update: The modified while loop could look like this:

while (my $line = <$rfh>) {
    chomp $line;
    if ($line =~ m/^HEADER/) {
        my $number = 42; # change to whatever number you want to use
        $line .= $number;
    }

    if ($line =~ m/^REMARK/) {
        print {$wfh} "Extra line\n" # Change to whatever extra line yo
+u want
    }

    print {$wfh} $line, "\n";
}
[download]