Issue #3325807 by kishan@lnwebworks, jsacksick: Ensure the variation reference...

  public function submitForm(array &$form, FormStateInterface $form_state) {

    $variations = $this->product->getVariations();

    $new_variations = [];

    $variation_groups = [];

    // Multiple variations can have the same weight, group the variations per

    // weight, and then iterate on variation groups below to reassign a correct

    // weight.

    foreach ($form_state->getValue('variations') as $id => $value) {

      $new_variations[$value['weight']] = $variations[$this->variationDeltas[$id]];

      $variation_groups[$value['weight']][] = $variations[$this->variationDeltas[$id]];

    }

    ksort($variation_groups);

    foreach ($variation_groups as $variations) {

      foreach ($variations as $variation) {

        $new_variations[] = $variation;

      }

    }

    $this->product->setVariations($new_variations);

    $this->product->save();