The laws regarding controlled substance prescriptions transfers are very strict and vary depending on the state you live in.
It is a federal law that when transferring a controlled substance prescription, it can only be done on a one fill basis (i.e. no refills). So while your new pharmacy may only be showing one fill remaining, you most likely have the remaining refills at your old pharmacy.
Unfortunately, there are many state laws which are more strict than federal law and a pharmacy must follow the stricter law. In New York for example, controlled substance prescriptions are not allowed to be transferred for any reason. Your doctor MUST provide a new prescription to the new pharmacy.
It's difficult to tell from your question if you are confused about why you were only allowed one fill of alprazolam at the new pharmacy or whether or not it was allowed one fill at all.
As mentioned, if you are in a state where the federal law is applied, you should be allowed to fill the transferred prescription ONCE only (old refills may still be available at your prior pharmacy). If you are in a state that allows no transfers, they may have simply put the drug on your profile to indicate it was current therapy for you, but were unable to actually fill it due to it being a controlled substance.
In situations like these, pharmacies should let their patients know about the rules and regulations of prescription transfers, but it often doesn't happen which can lead to confusion. Be sure to check with your pharmacy regarding the laws they must follow to get a better understanding of what is going on, for now and for future transfers.