According to Naviance, it appears my recommender submitted my letter of rec to two of the UC’s I am applying to, despite them not considering LOR’s for admission. Will the university just ignore the letters or should I write each of my schools an email explaining?
They are going to ignore them since they are not required. But they may be required for a specific major so maybe your recommended can submit them to that department that may require additional application.
Go with the assumption that this isn’t your counselor’s first rodeo. If indeed the letters were submitted, there was probably a good reason for doing so.
For the UC’s, LOR’s are only asked for by invitation so if they receive them and are not necessary, they will be ignored. Not even sure how they were submitted since you need a student portal sign on with a specific link to download them. The application is not even open yet to submit, let alone you having a portal to allow the submission.