Your posted code fails compile with the error

Missing $ on loop variable
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Please make sure that when you post code, it literally replicates your issue -- see How do I post a question effectively?.

If I run the code:

my %lengths = (
    1 => {x => 1,
          y => 2,
          z => [1,2,3],
         },
    2 => {x => 2,
          y => 3,
          z => [2,3,4],
         },
    3 => {x => 4,
          y => 5,
          z => [5,6,7],
         },
);

for my $coord (keys %lengths) {
   for (@{$lengths{$coord}{z}}) {
      print "$_\n";
   }
}
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I get the output

1
2
3
5
6
7
2
3
4
[download]

which seems to be your spec. My best guess is that you've got a typo in the code you are actually running, so that you aren't accessing the array. Try checking Data::Dumper after your loop to see if you are getting bitten by autovivification.