My recommender received the list of schools I would be applying to months in advance. She submitted 7 out of 10 letters and then just disappeared: ignores emails and notifications from schools. Why would anyone agree to write a letter and then do that? I have months of research experience under her indirect supervision and took her class too. She does know I have more than 3 referees though...
You're right that there isn't any particular reason for a professor to intentionally and voluntarily refuse to send letters to certain institutions, especially not without telling you.
So I would consider unintentional and involuntary explanations.
The notification emails may not be reaching her (IT failures, spam filters, etc). Try to contact her personally (email, phone, in person) and let her know that the letters are due.
Oversight is a possibility. She might have forgotten about the letters and then gone on vacation where she doesn't see the emails.
She may be unable to work because of some sort of emergency (personal, family, medical, etc). Recommenders are people too, and sometimes things happen in their lives that take priority over your letter. If you cannot contact her yourself, contact her institution or department and explain the situation. It is possible that they will have access to a letter she's already written and can send it out, or that someone else there can write a letter.
Is there any pattern to the ones she didn't submit? For example, are they the most competitive schools? If so, she could be cowardly refusing to recommend you for those programs.
Otherwise, I would agree with the other answers and comments; it is probably an oversight or some other factor that has nothing to do with you.