just to expand Devon's answer, which is perfectly correct...
this is due to a VCF format constrain, which states that 0 must always be the reference allele. this doesn't mean that the reference allele must be in a particular sample, it just means that a particular base is used as reference by a scientific community agreement.
in case you're working with human samples, this agreement is now supported by the Genome Reference Consortium, and I really hope that when the time comes (we shouldn't be that far) they'll be able to build a consensus reference based on entire world populations allele frequencies, but meanwhile we have to stick to the current reference. current GRCh38 has already done some work in this direction though.
since humans are diploids, sequencing a particular position will give you a pair of alleles, and usually the reference will be 1 of that 2 alleles. but this is not always the case, and you may find (as you already did) that a particular position doesn't contain the reference allele. this is rare, but far from being impossible due to the lack of population genetics evidences in the reference selected, as explained previously.