push @allmolecules, %imolecule;

I suspect the above line is not what you want to do. The 1st element of the allmolecules array is a key of the imolecule hash. The 2nd element of the array is a value of the hash. The 3rd element of the array is a key of the hash, etc. So, as you loop through the array, $allmolecules[$i] alternates between being a simple scalar and a reference to an array; it will never be a reference to a hash because %imolecule does not contain any hash references as its keys or values.

To debug, I like to reduce my code as much as possible, then print data structures, as follows:

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

my @maxval = 0 .. 4;
my %imolecule = (
        'maxval' => [@maxval],
        'peers' => '0',
          );

my @allmolecules;
push @allmolecules, %imolecule;
print Dumper(\@allmolecules);

__END__

$VAR1 = [
          'maxval',
          [
            0,
            1,
            2,
            3,
            4
          ],
          'peers',
          '0'
        ];
[download]

See also Basic debugging checklist and perldsc.

I can not reproduce your exact error message. If you can reduce your code to a smaller size and make it self-contained so that anyone can run it, then we should be able to give you better advice. Remember to use strict and warnings.