A tooth with a root canal isn't supposed to hurt

Last week I was on a cruise to Hawaii, which you can read about on my travel blog: http://travelinggiraffe.blogspot.com, when my tooth that had the root canal started to hurt. On Thursday morning when I was having breakfast I started to notice a bit of pain in my tooth that had just had the root canal, but it wasn't enough pain to alert me to trouble. When I had lunch though it was bothering again and worse. I texted my dentist and she wasn't sure what was wrong and offered to call in a prescription for Amoxacilain. In the end I decided against that and instead took pain medication and went to the dentist this morning. He took out the temporary filling looked inside, filled the tooth and said this - either the tooth was just irratated by something and will start feeling better later today, if not then it has a secondary infection. So far it's feeling a little better, but I only ate one meal so far.