Im convinced something is wrong with one of my students? what should i do? Im sure shes still suffering?

I would say leave her alone. She has talked to you in the past about the abusive situations she has been in, and she will talk to you again if she wants to. It could have been anything. Maybe her boyfriend sent a text that upset her. Maybe it was a friend. Something upset her, and it sounds like she was looking for an excuse to leave, but it may well have been a typical 16 year old problem. When she comes back to class you can ask if she's feeling better, and if everything's all right, and if she says yes, leave it at that. If she tears up again, and seems upset, you can ask her if she wants to talk. I wouldn't do more than that.