PHP CodeIgniter Bug Fix

General information for the website: We sell Guided Tours online
Description of requirements/features: This is one simple bug that is probably just one line of code.

The site uses the CodeIgniter framework. It utilises url-routing so that depending on the structure of the url, the user gets back from the database the correct page. Everything was working fine.

However, a few months ago I wanted to make a custom 404 page. I did this and everything looked fine. When users navigated through the site, the correct page appeared. When they tried to go somewhere that didnt exist, the custom 404 page was displayed.

HOWEVER although that's what was happening on the surface to the user, the bug is that even when the correct page is found and returned from the database, the http server status response is set as 404 error. It should obviously be 200. I checked this by using the POSTMAN extension in chrome.

I dont understand why it's happening and am too busy to look at it in detail. It is probably something very simple. However, this is important as the result of having a server 404 error is that my pages are de listed from all search engines and cannot be re-indexed!!!
CMS and Admin requirements: CodeIgniter familiarity a bonus
Similar urls: http://citylightstours.com
Extra notes: I have another site that uses virtually exactly the same code but it is working fine.