My professor thinks I deceived her, but it was miscommunication on my part. Should I send an apology email?
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.