I had a menu in which I juste added 3 items but instead of having :

<div class="avia_mega_div avia_mega2 six units">

<ul class="sub-menu">
    <li id="menu-item-2016"></li>
    <li id="menu-item-2955"></li>
    <li id="menu-item-2017"></li>
</ul>

</div>

I had that :

<div class="avia_mega_div avia_mega2 six units">

<ul class="sub-menu">
    <li id="menu-item-2016"></li>
    <li id="menu-item-2955"></li>
</ul><ul class="sub-menu avia_mega_hr">
    <li id="menu-item-2017"></li>
</ul>

</div>

As I didn't find why I corrected with javascript. But now I have some woocommerce checkout custom fields (Checkout Field Editor for WooCommerce plugin) at the wrong place (wrong order) I don't know if it is the same cause, I checked with add_filter("woocommerce_checkout_fields" and there's no problem here EDIT: there are in the wrong order here too).

I tried to disable plugins one by one but didn't find one causing the problem.

How can I "ascend" the issue to find the cause ?

EDIT: I created a woocommerce_checkout_fields filter, reordered the fields and reseted the "order" and "priority" properties, it corrected the issue. Some fields had no "priority" property but the "order" one. I think the custom fields editor plugin uses order when the new WP uses priority.