You should actually write a stand alone code snippet that shows the problem. With your code as posted:

$string = "atccatccctttaat";
@triplets0 = $line=~ /(...)/;
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we can't tell what result might be expected because we don't know what the content of $line is. We could assume that you intended $string, but that wouldn't give the results you describe. Start with the following code and recreate the problem you saw, then post that code:

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

my $string = "atccatccctttaat";
my @triplets = $string =~ /(...)/;

print Dumper (\@triplets);
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which prints:

$VAR1 = [
          'atc'
        ];
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as expected