Educated guess:

// Put all values in an array().
$AllItems = array_merge($FruitsCategory, $DrinksCategory, $DrinksCategory); // use array_merge

foreach ($AllItems as $Item) {
  $article->field_article_all_items[] = ['target_id' => $Item];
}

$article->save();

Educated guess: (The key was to merge the arrays by using array_merge())

// Put all values in an array().
$AllItems = array_merge($FruitsCategory, $DrinksCategory, $DrinksCategory); // use array_merge

foreach ($AllItems as $Item) {
  $article->field_article_all_items[] = ['target_id' => $Item];
}

$article->save();

Also it can be used within the node creation:

// Put all values in an array().
    $AllItems = array_merge($FruitsCategory,$VegetablesCategory,$DrinksCategory);

// Create a new "Article" node.
    $article = \Drupal\node\Entity\Node::create([
        'type' => 'article',        
        'title' => Test,
        'langcode' => 'en',
        'uid' => '1',
        'status' => '1',
        'created' => $current_time,
        'field_article_all_items' => $AllItems,  // use array_merge
        ]);
// Save the created node.
    $article->save();

Educated guess:

// Put all values in an array().
$AllItems = array_merge($FruitsCategory, $DrinksCategory, $DrinksCategory);

foreach ($AllItems as $Item) {
  $article->field_article_all_items[] = ['target_id' => $Item];
}

$article->save();

Educated guess:

// Put all values in an array().
$AllItems = array_merge($FruitsCategory, $DrinksCategory, $DrinksCategory); // use array_merge

foreach ($AllItems as $Item) {
  $article->field_article_all_items[] = ['target_id' => $Item];
}

$article->save();