I encountered the same issue. I tried to investigate different scenarios with various colleagues. If a user upgrades directly from an iPhone running iOS 16 or earlier to iOS 18, or uses the migration feature to move to iOS 18, the certificate does not appear in the Certificate Trust Settings (Full Trust for Root Certificates) list. However, the same certificate can be successfully installed on an iOS 18 device that hasn’t gone through migration or on a device that has upgraded from iOS 17 to iOS 18, where it appears normally in the Certificate Trust Settings list. We attempted many solutions and initially thought there might be an issue with our certificate. However, we then directly installed Apple's official Apple PKI webpage (https://www.apple.com/certificateauthority/) and downloaded a certificate for testing. We found that devices with these issues also failed to display the certificate in the list for enabling it. Currently, the only workaround is to reset the entire phone and not use the migration feature or upgrade from iOS 16 or earlier to iOS 18. Only then will the certificate display correctly in the Full Trust list. I'm not sure if this bug will be fixed.