The first year is a tornado of emotion, and none of it is good.
Try to remember that she's not the one "making things worse." She's just an involuntary participant on the worst mental and physical roller coaster imaginable.
It's ok for you to feel worried or uncertain, but something that is critical to healing is that you be her rock. When she's angry, when she's sad, when she's scared... don't ask her WHY. It will be the same answer again and again. Hold her every day and tell her you're not going anywhere no matter what.
The first year, BS's are desperate for some kind of foundation. We want to trust you but we are suffering from betrayal and with that comes anger. It's not from left field, it's fallout from the affair and there's YEARS of that to sort through.
You don't have to perform miracles. You do have to get over being defensive. Right now, it's not about whether you're upsetting her purposely or not. She's hemorrhaging emotion. Just hold her, apologize, and tell her you love her.
Crazz did this for me and it helped slowly bring me out of the dark. I'm speaking from experience. You can do this.