How to avoid this malicious links issue?

Upgrade your website to latest version if it is developed in WordPress or Joomla and clean the website by deleting malicious links from the website. Also you can use Acunetix Web Vulnerability Scanner which is an automated web application security testing tool that audits your web applications by checking for vulnerabilities like SQL Injections, Cross site scripting and other exploitable vulnerabilities.

In general, Acunetix Web Vulnerability Scanner scans any website or web application that is accessible via a web browser and uses the HTTP/HTTPS protocol. Acunetix Web Vulnerability Scanner offers a strong and unique solution for analyzing off-the-shelf and custom web applications including those utilizing JavaScript, AJAX and Web 2.0 web applications. Acunetix has an advanced crawler that can find almost any file. This is important since what is not found cannot be checked.

How Acunetix Web Vulnerability Scanner Works?

Acunetix Web Vulnerability Scanner works in the following manner:

•  The Crawler analyzes the entire website by following all the links on the site and in the robots.txt file and sitemap.xml (if available). Web Vulnerability Scanner will then map out the website structure and display detailed information about every file.
• If Acunetix AcuSensor Technology is enabled, the sensor will retrieve a listing of all the files present in the web application directory and add the files not found by the crawler to the crawler output. Such files usually are not discovered by the crawler as they are not accessible from the web server, or not linked through the website. Acunetix AcuSensor also analyses files which are not accessible from the internet, such as web.config.
• After the crawling process, Web Vulnerability Scanner automatically launches a series of vulnerability checks on each page found, in essence emulating a hacker. Also, Acunetix Web Vulnerability Scanner analyses each page for places where it can input data, and subsequently attempts all the different input combinations. This is the Automated Scan Stage. If the AcuSensor Technology is enabled, a series of additional vulnerability checks are launched against the website.
• If AcuSensor Technology is used details such as source code line number, stack trace or affected SQL query which lead to the vulnerability are listed.
• In addition, a port scan is launched against the web server hosting the website. If open ports are found, Acunetix Web Vulnerability Scanner will perform a range of network security checks against the network service running on the open port. If open ports are found, they will be reported in the ‘Port Scanner’ node. The list of open ports contains information such as the banner returned from the port and if a security test failed.
• After a scan has been completed, the scan results can be saved to file for later analysis and for comparison to previous scans. Using the Acunetix reporter a professional report can be created summarizing the scan.

There are multiple reasons using which Trojans can be injected into server. Although we have disabled ports 31337 and 12345 on which Trojans run normally but it can be injected using other ports also. Hence, blocking each and every port on a shared server is not feasible option due to which web server cannot provide proper web services.

For further details you can refer below mentioned URL.

URL: https://www.howstuffworks.com/trojan-horse.htm
* Acunetix (Free trail available) is a third party website and there is no relation between QualiSpace and Acunetix