The problem is that as you remove elements you invalidate the index that you are using. However, Perl has a much better way of doing what you want. Consider:

use strict;
use warnings;

my @arry = (9,0,0,5,3,0,0,0,2,0,1,0);
print "@arry \n";
@arry = grep {$_} @arry;
print "@arry \n";
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Prints:

9 0 0 5 3 0 0 0 2 0 1 0 
9 5 3 2 1
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The magic is grep.