So, in trying to really come back after one-two years of general inactivity, I've been grabbing nice pets and breeding them together.
I hatched an egg today from two pets that I bred before deciding to begin breeding better 6vis babies, and 2/3 of his genes do not belong to his parents.

Father (Mintberrolate... I was bad at naming, it seems.)
Gene One: (DD) Back Stripes
Gene Two: (BB) Fallow Deer
Gene Three: (FF) Mystic Runes

Mother (Spring Angel)
Gene One: (GG) African Painted
Gene Two: (BB) Fallow Deer
Gene Three: (CC) Life Runes

Offspring (Un-named as of now)
Gene One: (EE) Regal Markings
Gene Two: (CC) Witch Doctor
Gene Three: (CC) Life Runes

Why does he have Regal Markings and Witch Doctor? Do earlier generation's genes play a role?
Here is his lineage, if you'd like to look: Click

Edit: Just had another instance with Witch Doctor. Mother has Fallow Deer, father has Kitsune.

Also, as a side note. I've been stuck on one point of the world map since forever. I can't beat the Nightfall Bandits in the Fungus Grove! I'd like to know what I can do to overcome them, along with my original question above.

When you look at a pets genetics, you will see that they have a 2 letter "code" next to the trait name. This is bcaue pets can be born with what are called "hidden traits", which are traits that are hidden under a more dominant visible trait. You can only see thee if the pet is tested.

When each ept is bred, each parent passes on either one of those letters for each slot. ("N" means there is nothing there, so NA would be a carried of the gene that corresponds to A whereas AA would have that trait visible) so if you breed an NA pet to a BB pet, that offspring will be born with either NB or AB.

So in that particular example, if the offspring was born with AB, it would have the A trait visible but also be able to pass on that B trait to an offspring. So if you enxt bred that AB offspring to a CC pet, you could AC or BC as the offspring.

again, you can only see hidden traits when the pet is tested.

If you look back to the grandparents of your particular pet, you can see that the grandparents do have those traits. So it looks like the more recessive traits just got carried up under those more dominant ones (alphabetical order) until you got a lucky draw and the baby got those passed on instead of the more dominant ones.

Thank you for the help! Although I know about alleles and the hidden traits, I didn't know that it doesn't show those recessive traits unless an item is used. Thanks, again.