In the Quartus® II software version 15.0 and earlier, attempts to trigger a Nios II Interrupt exported from a Qsys subsystem within a hierarchical Qsys main system will be unsuccessful.
Instead of directly exporting the Nios II Interrupt Receiver signals, connect them to a IRQ Bridge Interrupt Sender. Then, export the IRQ bridge Interrupt Receiver to the top level Qsys main system. In this way, Nios II will be able to receive interrupts sent via the IRQ Bridge.
Alternatively, create the Nios II system directly in the Qsys main system instead of a Qsys subsystem in a hierarchical arrangement.
This problem is scheduled to be fixed in a future version of the Quartus II Software