Not really, anonymous. Just as humans come in a wide variety of different heights, so too do pokémon. The average you might see listed in the pokédex is merely an average: the average height of a pokémon species, as determined from data collected through a large sample. In truth, only a handful of flygon are actually 6′07″; they are otherwise a wide variety of different heights, from 4′00″ all the way up to 8′00″. There’s only something wrong if your flygon is excessively small or large, and that’s only because such heights can be linked to actual medical problems that your local Nurse Joy would have diagnosed by now.
In short, anonymous, your flygon may be perfectly fine—just a bit on the shorter side than most.