I am receiving the message from Forticlient saying that windows requested a reboot so that it can finish installing updates and you must reboot your PC to allow Forticlient to finish the vulnerability patching.
Is there a way that we can disable these pop-up for end user machines.
Well, the whole point of Vuln Scan in my opinion is to resolve the issue(s) by installing the required patch(es) which might require a reboot just like windows updates, not just detecting them, otherwise you can just disable Vulnerability Scanner all together or just Automatic Patching.