The chomp documentation specifies that the function "removes any trailing string that corresponds to the current value of $/ (also known as $INPUT_RECORD_SEPARATOR)", which defaults to the newline character, \n.

I'm not sure what those characters are, but when I am trying to identify unusual characters, I use the ord function:

#!/usr/bin/env perl
 
use warnings;
use strict;
my $str = 'abcde';
for (split //, $str) {
    print "$_:", ord $_, ":\n";
}
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Once you identify the characters, it will be easier to figure out a way of eliminating them.