So it appearc that the pipe is being put at the beginning of the line by the hash, I have no idea why?

As others wrote, hard to say without seeing the code. But hard to believe too:

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my %hash=(foo => 1, bar => 2, baz => 3);
$hash{$_}="|$hash{$_}|" for keys %hash;
print Dumper \%hash;

__END__
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So it appearc that the pipe is being put at the beginning of the line by the hash, I have no idea why?

It's hard to believe that the hash is putting anything "at the beginning of the line". And no, I don't know if you have no idea why.