Quartus Prime Pro Edition software erroneously applies location assignments and constraints to I/O pads instead of logical pin names

In the Quartus^® Prime Pro Edition software, the I/O pad atom does not replace the logical pin name. Instead, the I/O pad atom is inserted in between the logical pin name and the rest of the logic, and it has the suffix ~pad.

All assignments made to the logical pin name, including location constraints, are automatically applied to the pad. For example, the logical pin named clk has a corresponding pad called clk~pad. If you have a location assignment to clk, the assignment is applied to clk~pad instead of clk.

There is no workaround. This issue will be fixed in a future release of the Quartus Prime Pro Edition software.