How can I wrap form content in bootstrap divs?
The way you are suggesting works fine. (I just tested it). Try to clear your cache and hard refresh the page. If you do: 

&lt;div class="my_custom_class"&gt;&lt;input{{ attributes }} /&gt;{{ children }}&lt;/div&gt; 


you will have your form inputs wrapped in that div.

The other options is to use the form-element.html.twig or you can use the hook_form_alter and add prefix and suffix to your fields.