To work around this problem, combine the Qsys systems into a single Qsys system.
If you unable to combine the Qsys systems then follow these steps:
1) Move the affected Qsys files to the top and bottom of the file list
2) When you see the first affected qsys finish elaboration, navigate to the folder /db/ip/<qsys_project>/submodules and delete alt_cusp151_package.vhd before the second Qsys system elaborates
This problem is scheduled to be fixed in a future release of the Quartus Prime software.