Final answer:
The error likely occurred because the developer may have used Java applets, which run in a sandbox environment and restrict access to system resources, conflicting with the intended functionality of ActiveX scripts.
Step-by-step explanation:
The most likely cause of the design flaw regarding the restriction of the code's access to resources within the user's computer, despite efforts to enable interaction with ActiveX scripts for digital certificates and trusting certificate authorities, is that the developer may have inadvertently used Java applets. Java applets, which run in a sandbox by design for security purposes, would restrict the code's access to the system's resources, hence hindering the intended functionality of the ActiveX scripts.
This scenario aligns with the nature of Java applets within web development, where they are executed under strict security constraints to prevent unauthorized access to the system resources of the user running the applet in their browser.