My professor thinks I deceived her, but it was miscommunication on my part. Should I send an apology email? I will try to keep the situation short, but I am currently not on the best of terms with a graduate school professor.

The term is over now and I have been on good terms with her until today. As part of this course, students must attend an extra set of lectures outside of class and write a very brief report (mainly as proof we had actually attended and analyzed the topic). There was one lecture I was unable to attend due to a conflict with a class and thus informed my professor (in person) on two occasions. She had told me that she would upload the transcript for the presentation online. Yesterday, I had read the transcript and submitted my brief report.

However, she soon contacted me via email and requested I call her. During the phone conversation, she had accused my of deceiving her by pretending I had attended the lecture. I had explained to her that I had read what she posted online as I was unable to attend it. She said that, since I had not explained this in my email, she does not believe me. I do not think our phone conversation ended very well.

This is a very "subjective" course in that her opinion determines our grades. I am wondering if it would be wise to send her an apology email clarifying that it was simply miscommunication on my part?
Whether you can meet with her or not -- and I suggest you try, even if it were via Skype -- I would recommend sending her an email laying out your side. If you do receive a poor grade and you need to seek redress through some formal process, email is evidence that you attempted some explanation. The merit in your explanation is, of course, quite another matter.

Good luck.