URL structure is different in Apache and NGINX. WHY?????

Question

I have hosted my site on NGINX server and site is working well and no issue detected but one thing is found that is different in apache and NGINX for q2a site.

URL structure is different in NGINX as compared to apache.

URL in Nginx for question page is 

<script src="../../qa-content/jquery-3.3.1.min.js"></script>

<script src="../../qa-content/qa-global.js?1.8.3"></script>

<script src="../../qa-plugin/wysiwyg-editor/ckeditor/ckeditor.js?1.8.3"></script>

But in Apache server for same question pages the url parrent is

<script src="../qa-content/jquery-3.3.1.min.js"></script>

<script src="../qa-content/qa-global.js?1.8.3"></script>

<script src="../qa-theme/SnowFlat/js/snow-core.js?1.8.3"></script>

I don't understand why it is happening. I tried to figure it out but did not get any conclusion on IT

Please Scott kindly make me understand.

Comments

Does the site work ok on both servers, or does one cause a problem?

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The site works on both the servers but the URL pattern is changed

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So what exactly is the problem?
Are you sure the URL you are loading is exactly the same, it's not in any subfolder?

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Yes, URL is exactly the same but the problem is the url structure in html as shown above in example.

The reason .htaccess do not work on nginx and I have modified .htaccess code given in default q2a to work in nginx and it was working perfectly but url binding changed.

There is no documentation in q2a how to properly use .htaccess rule in nginx.

Can you @scott please tell me the exact code for nginx to work .htaccess rule?