Previous employer possibly giving me a negative reference?

I previously worked for a well-known medical university in New York City, as an administrative assistant. It was a part-time position that only last five months, as I left the country for a Fulbright fellowship and quit - with over a month's a notice, and trained my replacement. Upon my return, and upon receipt of my Master's in Arts this June, I am currently applying to positions and using my previous supervisor as one of my references. While we did not have a stellar personal relationship, professionally, I was always on time, reliable, did my work and tried to not only meet but exceed expectations, and never called out. The previous girl in my position did not get along well with this supervisor, and even the HR department was privy to how difficult it was to get along with this particular supervisor (which is why it was so difficult to constantly fill the position). I've only been working after college for three years, but I've had shining references before this position, and I work hard to pay rent, tuition, etc. Recently, one of my prospective employers told me that they will be issuing me an offer letter after checking into my references. I emailed for follow up on said references, and got a response that said "Thank you for your interest, but we've decided to go with another candidate and made this decision yesterday." After asking this prospective employer about my references, she said they all got back to her - and I am personally under the impression that this particularly supervisor gave me a negative review, as all of my other references I still keep in close contact with. Plain and simple, what can I do to look into this matter further? I'm 25 years old and looking for "real" jobs now - I don't need this woman plaguing my track record of normally stellar performances. It was also a very good job and looks great on my resume, and I don't want to omit it. I know that it's a possibility that this company really did go with an internal candidate at the last moment, but I don't really believe that - what legitimate, well-reputed organization offers you a job, and then pulls out last minute, coincidentally just after checking your references? Any advice would be helpful - I am angry and frustrated, and I don't want this to be repeated with other potential positions.