Problem related to PIO component in SOPC system

I apologize if this is obvious, but I had a simliar problem because I made a very simple mistake of not constraining my clock and reset input pins for my development board. When I would add a peripheral, the automatic assignment would move the clock somewhere else and I would get an error like you described. I used the Pin Planner to assign the clock and reset pins, and I had no more problem with it. You also have to make sure your LED outputs are assigned to the right pins for your board.