Upload Multiple Files With Multiple Fields And With media_handle_upload

code from my theme adjusted to you 

<fieldset class="images">
<input type="file" name="my_file_upload[]" id="my_file_upload[]" multiple="multiple">
</fieldset>
<fieldset class="memes">
<input type="file" name="my_file_upload[]" id="my_file_upload[]" multiple="multiple">
</filedset>

and its working

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