It only populates the hash with #4.

That's because you do

@populations = (4);
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Now you what do you have in @populations? Exactly one element, the 4. You iterate over that, and the loop is executed once setting $_ to 4.

Inside your loop, you do

        %HoH = (
            @populations => {
                individual   => "@ind",
                chromasome1  => "@chroma",
                chromosome2  => "@chromb",
            },
        );
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which resets %HoH at each pass. Well, it would, if you had more than one element in @populations.

I guess you mean something like

use strict;
use warnings;

use Data::Dumper;

@populations = qw(mice cats dogs potatoes);
    
my %hash = gener(@populations);    
    
sub gener {    
    my @populations = @_;
    my %HoH;
    for (@populations) {
        my @chroma = (0...10);
        my @chromb = (0...10);
        my @ind = (0...10);
        $HoH{$_} = {
            individual   => \@ind,
            chromasome1  => \@chroma,
            chromosome2  => \@chromb,
        };
    }
    foreach my $population ( sort keys %HoH ) {                       
+ 
        foreach my $info ( sort keys %{ $HoH{$population} } ) {       
+     
            print "$population: $info = ",
                join(', ', @{$HoH{$population}{$info}}),"\n";
        }
    }
    print Dumper(%HoH);
    return %HoH;        # returned as list; to returna ref, use \%HoH
}
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