If I try the list util it doesnt work

Not enough information there. Error message? Segfault? Compilation error?

What is wrong/missing here?

This line:

@trips = join(" ", @trips);
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ruins it. What do you understand this line to be doing? Without it I get at least some shuffling which may or may not be what you want:

#!/usr/bin/env perl 
use strict;
use warnings;
use List::Util 'shuffle';

print "enter sequence and signal end with enter followed by ctrl d\n";
my $sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
my @trips = unpack("a3" x (length($sequence)-2), $sequence);
my @shuffled = shuffle(@trips);
print "@shuffled\n";
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which gives:

$ perl /tmp/shuf.pl 
enter sequence and signal end with enter followed by ctrl d
aaabbbcccddd
sequence inserted : aaabbbcccddd
ccc aaa    ddd  bbb
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I am on perl v5.18.2, so the list utils should already be there you mention?

Yes.