Due to limitation of available HPS IO pins in U19 package (484 pin count), HPS USB0 cannot be routed to HPS IO Pin Mux. If a user tries to select USB0 to be routed to HPS IO Mux, Qsys will prompt an error of "Peripheral USB0 has an illegal mode set". USB1 is not affected by this limitation.
Device Family: Cyclone® V SE
In the Quartus II software version® 14.0 and later, if the device assignment contains a Cyclone V SoC device with U19 package, Qsys will show USB0 as "Unused" in the drop down option. USB1 is not affected and can be routed to HPS Pin Mux. If users require two USB controllers, they will need to use a larger package in their device assignment.