use strict; use warnings;. You use %hoh in the first code sample and %HoH in the second.

{$HoH{1}{'individual'}} tries to generate an anonymous hash but only provides one element - a hash requires pairs of elements. Very likely you intended my @value = @{$HoH{$counter}{'individual'}}; to cast the array reference to an array.

Possibly the overall code you are looking for is something like:

use strict;
use warnings;

my %HoH;
my @newind = (1 .. 3);
my @newchroma = (4 .. 6);
my @newchromb = (7 .. 9);

$HoH{1} =
    {
        individual  => [@newind],
        chromasome1 => [@newchroma],
        chromasome2 => [@newchromb],
    };

my @value = @{$HoH{1}{'individual'}};
print "@value \n";

$value[0] = 42;
$HoH{1}{'chromasome1'} = [@value];
print "@{$HoH{1}{'chromasome1'}}\n";
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Prints:

1 2 3 
42 2 3
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