I can say that I only put one country, and at the time of interview it became a point of some questioning, but nothing bad, just curiosity about which passport I used the most or most recently, because I brought both passports to the interview. However, if the instructions (which I guess didn't read carefully) say to include countries, then I see no harm in listing both countries. However, the the question about which country issued your last passport is pretty clear, check your passports and choose the one which issued your passport more recently.