Custom fields changes the formatting of metabox input

The whole point of esc_attr is to encode special characters to avoid confusion later on. So if you have double quotes, yes they will be changed into ". If you don’t want that, don’t use esc_attr.

If you insist on using esc_attr but don’t like what it does, you’ll have to undo it after you have used it. That would go like this:

$input = esc_attr ($_POST['alep_textfield1']);
$input = str_replace ('"', '"', $input);
update_post_meta ($post_id, 'alep_textfield1', $input);