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Thank you for the reply Admiral! The MSPE will indeed be corrected, but the initial transcript with the error on it is still uploaded to ERAS. My school will be replacing this with a new transcript soon, but my fear is that some programs may have already reviewed my file with this mistaken red flag in it.
I hope that clears up my question further!
There's a typo in your initial question, which is the confusion. You mentioned your MSPE and your Dean's letter, which are the same thing. You meant your MSPE and your transcript.
Although my answer to the question "Should I contact programs and tell them about XYZ change to my application" is essentially universally "no", this may be a case where the answer is yes. Some programs might disqualify applications with anything failed. In fact, the more minor the course, the bigger problem it might be. Fail a shelf exam and need to remediate -- some programs may not care. Fail "Professionalism" or "Ethics" or "Learning to be a doctor" -- courses that should be simple to pass -- suggests that you have a real problem, or that you're lazy, or that you don't take deadlines seriously. So alerting them that there was a mistake on your transcript may be very necessary -- as programs may have already decided to not look further at your application.
Best case scenario is that your school does the contacting -- it's their mistake (perhaps), if they reach out it looks even better. They may decline to do this, and then you probably should. Apologize for the inconvenience (even though it's not your fault), mention that there was a course marked "fail" incorrectly and it's been updated, and ask them to re-evaluate your application if necessary. The more competitive fields/programs you're considering, the less this is a concern -- they probably will wait for the MSPE anyway.