Friendship problem with a close friend

So this is the first time I'm in a problem where my close friend has been mad at me. Recently I had a problem with my best friend, it has been sorted out, and my close friend helped me. But at lunch I was with her and a few other people then someone littered. My close friend got mad at them ,she is really passionate about the environment and such, and asked them to stop. They told her no so then she just walked away n frustration. I didn't follow after her, which I should have done. At the end of the day, she asked to talk to me and went straight up in my face and said,"You and (my best friend) made me feel like sh*t today." then walked off to go home. I'm a timid person so I couldn't apologise on the spot and now I feel really bad. I'm honestly not sure what to do in this situation since it's the first time I had a quarrel with her. Having this situation happen now makes me wonder if I'm an oblivious and bad friend after realising the last incident I the class I sit next to her in?