I believed this issue is coming from similar design as posted in here (please correct me if I'm wrong) : https://forums.intel.com/s/question/0D50P00004fKxtM/is-this-the-bug-of-altmemddr-ip-of-intel
Again, it’s hard to tell Quartus warning is coming form NIOS II or ALTMEMPHY IP without reviewing the design.
Anyway, please try to remove NIOS II from design and see how many warning is left with ALTMEMPHY IP? This will help to separate out warning between NIOS II and ALTMEMPHY IP. The reason I request this is because currently we serve forum case per area basis. As for me, I work on EMIF IP area. For new issue like NIOS II or qsys connection, I sincerely appreciated if you can file new case for this separate issue then the system will assign to the right application engineer to support you. As for IP area, I will continue to work with you 😊
Just to share my suggestion here. Have you consider to upgrade to UNIPHY IP instead ALTMEMPHY IP as ALTMEMPHY IP is already EOL. Plus, there won’t be any further support for ALTMEMPHY IP . The best I can do is helping to workaround the issue.
Let me know your feedback