Recovery & Healing

I was with my partner for 5 years. Along the way, we have hurt each other in different ways but loved each other tremendously. We got into the biggest fight and broke up. It has been a month and a half since we last saw each other. We have been civilised in our emails since the break up, one, clear the air and closure of the lesson we need to learn and to work on ourselves in order to love healthily - and two, for me to go over the house to spend time with our cats. After therapy, reading self help books, participating in self help talks I realised I have made a lot of mistakes towards her [my focus is my mistakes and not the other person's]. I decided to call her and apologized. Nothing about working things out or wanting us back etc. Purely, apologize on all the ways I have wronged her. I believe strongly that you have to ask for forgiveness even if the voice shakes and only then can we forgive ourselves. She was quiet, she cried and said she cannot talk to me too long as it was giving her stomach ache and she said she was happy that I am doing this therapy for myself. I wasn't entirely finished but I didn't want to be forceful either. So I said I understand and for her to have a good rest. My question is... Why did she cry and why couldn't she talk to me?