Maybe add some parameter validation to your subroutine to catch out of bound errors?

sub popnum3 {
    my ( $x, $y, $z ) = @_;
    warn "y=$y is out of bounds" if $y - 1 > $#aob || ! ref $aob[ $y -
+ 1 ];

    my @row  = @{$aob[ $y - 1 ]};
    my $mean = mean(@row);
    $aob[$x][$y] = $mean * ( 1 + $z );
    return $aob[$x][$y];
}

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Update: Meant to be reply to OP

In reply to Re^2: undefined value in array reference by wind
in thread undefined value in array reference by Dandello

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