No sequencing technology is perfect. For the full sequence mtDNA test, FamilyTreeDNA uses a Next Generation Sequencing technology called Illumina. I will vastly oversimplify here, but this method determines the sequence by extending fragments of your DNA sample, applying fluorescent tags, and detecting the wavelength of light produced as each nucleotide is added. Each nucleotide type fluoresces at a different wavelength, and the computer "reads" the wavelength to determine the base.
On rare occasions the wavelength detected may be ambiguous, not due to any fault of the sample or the sequencer. Certainly there is not a defect in the DNA. Illumina is a very accurate sequencing technology, but there will always be the occasional error or ambiguity.
Retesting the sample may provide you with a more definitive result, but may not. However, I do not really see an issue here. You know that the missing nucleotide is a purine, most probably guanine. If you feel that this one nucleotide (out of the 16,000+ mtDNA nucleotides) is very important in your analysis, then by all means contact FamilyTreeDNA to find out if they will re-run your sample to get a more definitive result.