The article mentions this could be a genetic flaw (the article implies mutation), but I'm not so certain of that.
Malformations of the head due to errors in positioning genes (aka Hox or Sonic Hedgehog) generally, but not always, have relatively global effects. For example, mutations in
shh affect not only facial positioning but brain development as well. I would think it would be immediately obvious if there were developmental problems in the deer. Most of all, I don't think it would have survived.
My guess would be some sort of parasitic infection during embryonic development or possibly (but unlikely) early childhood which messed development. This is far from an uncommon phenomenon in nature - you see it in frogs fairly often, for example. It could also be some sort of environmental pollution causing mutation... but those mutations are far more often than not more devestating and harmful to development.
Another guess would be that this is simply an extremely rare and selected against allele.
Anyway, I don't know enough about deer genetics or physiology to make any more than the most broad guesses. Sorry to be all biological, resume senses of wonder.
