If $element_count is an integer, then there's no reason to use a hash instead of an array. So what you really want is an array of arrays, thus.

$element_count = 0;
foreach $element (@CLIQUE_ID_START_LINES) {
if ($element != $CLIQUE_ID_START_LINES[-1]) {
      for my $i ($element..$CLIQUE_ID_START_LINES[$element_count+1]) {
        push(@{$CLIQUE_DETAILS->[$element_count]}, $VCONFIG[$i]);
      }
      $element_count++
}
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