You’ve altered the plugin PHP code without altering the plugin JS code that inserts the new value. Altering the core code of a plugin is not a good idea as you’re going to keep making these changes whenever there’s an update.
My suggestion would be to find a way to apply CSS to the HTML created by ACF instead of altering the HTML that it outputs.
What is it that you can do with
<li>
<input />
<label></label>
</li>
that you can’t do with
<li>
<label>
<input />
<span></span>
</label>
</li>
