It would randomly pop into her mind, these random incidents.
Emma would find herself thinking about Regina's reactions and then she started thinking of the aftermath. How the bruising or cuts didn't seem quite as bad as she would have anticipated. How quickly Regina seemed to heal.
At first she thought it was magic, but then realized that if that was the case there would have been no evidence. Regina would have healed herself instantly. Why was she letting it heal on its own at all?
It began to bug her. She would chew on it frequently. It got to the point where she knew she would need to address it soon with her son's other mother.
So she bid her time, knowing she'd have to catch Regina when she was vulnerable. Not an easy feat. But Emma would risk the Queen's wrath in order to quell the acid in her stomach.
Deep down she knew she would not like where this road would lead but as the Saviour she also knew she needed to be the one to find the answer.