splice with map could work, but the better approach if possible would be to catch it on the front end, and filter it; you may make optimizations once you get it working for your purposes. A possible improvement would be to replace the grep with List::Util's any function.

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

my @skip_idx = (6,13,42,66,69);
my @array = ();
my @invarray = ();

my $idx = -1;
foreach my $str ('aa'..'zz') {
  ++$idx;
  if (grep { /^$idx$/ } @skip_idx) { # could use List::Util::any here
    push @invarray, $str;
    print "skipped '$str' (index of $idx)\n";
  }
  push @array, $str;
}

print Data::Dumper::Dumper(\@invarray);
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Output,

$ perl test.pl
skipped 'ag' (index of 6)
skipped 'an' (index of 13)
skipped 'bq' (index of 42)
skipped 'co' (index of 66)
skipped 'cr' (index of 69)
$VAR1 = [
          'ag',
          'an',
          'bq',
          'co',
          'cr'
        ];
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