Due to a problem in the Intel® Quartus® Prime Pro Edition Software version 21.3 and later, you may see functional errors in an IO register that has a locally routed clock. The functional failures occur because the clock route is illegal and not analyzed for timing.
This problem only affects Intel® Agilex™ devices where there is a register in an IO cell whose clock is routed on local routing rather than a global clock net.
To work around this problem, either ensure that the clock is routed on a global clock net or that register is not in an IO cell.
Beginning with the Intel® Quartus® Prime Pro Edition Software version 22.1, designs constrained to implement a register in an IO cell with a locally routed clock will error out.
Patches are scheduled to be released that will add this error to previous versions.