If $group, $id, $stage etc don't exist in $coordinates, then that will auto-vivify them. You need to check the existence of each level in the hash if magically creating them merely by looking at them is a problem for your application. Something like this (ignoring your application's logic for the sake of making my example code clearer):

if(exists($coordinates->{$group})) {
  if(exists($coordinates->{$group}->{$id})) {
    if(exists($coordinates->{$group}->{$id}->{$stage})) {
      ...
    }
  }
}
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or to generalise (untested. haven't even tried to compile it) ...

my $result = do_stuff_in_hash_without_autovivifying(
  sub {
    my $hash_to_work_on = shift;
    # do stuff here
  },
  $coordinates,                 # initial hash
  $group, $id, $stage, 'coords' # list of keys to traverse
);

sub do_stuff_in_hash_without_autovivifying {
  my($sub, $hash, @keys) = @_;
  if(@keys && exists($hash->{$keys[0]}) {
    return do_stuff_in_hash_without_autovivifying(
      $sub,
      $hash->{$keys[0]},
      @keys[1 .. $#keys]
    );
  } else {
    return $sub->($hash);
  }
}
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If you're *really* paranoid about auto-vivification, then you can subvert Tie::Hash::Vivify to turn it into a fatal error instead of silent data corruption:

use Tie::Hash::Vivify;
use Data::Dumper;

my $hash = Tie::Hash::Vivify->new(sub {
  die("No auto-vivifying! Bad programmer! No bikkit!\n".Dumper(\@_))
});
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