I don't quite understand how the genes work in this game, when it comes to breeding and would love it if someone could explain it to me. Here's what I don't get:

If Parent 1 has the gene (AA) and Parent 2 has the gene (CC), the offspring should come out with the gene being (AC), as far as I know about how genes are supposed to work. Instead, I've had multiple cases where the offspring had (CC).
In another case, Parent 1 had (IJ) and Parent 2 had (JJ). The offspring ended up with (IJ) for its gene. I do understand that in a rare case, this one can happen. But rather than being rare, it has happened several times.

So, just how do genes get passed down in this game? What determined which gene is passed down? The first scenario, which has happened a few times now, has me pretty confused.

in cases such as the AA x CC = CC, the answer would have to be "parent AA is Untested and has a Hidden trait under the A that you cannot see because of this, with said trait's dominance being equal to or lower than C", since the site uses punnett square genetics

IJ x JJ offspring would be 50/50 IJ or JJ, which means IJ, in this case, is not rare (in the context of a single trait slot, the rarest chance there is is 25%, which is also... not really rare.)
(I'd say it only really starts getting 'rare' when taking multiple different trait slots into consideration at once, such as when you're doing 6v projects and trying to get multiple slots to throw you a 25% chance at one time)

guide post that has more indepth

Both parents are tested, which is why the AA + CC having a CC child is confusing.

what pets are the ones in question?

I can't locate them, so I'm starting to think either I saw it from someone elses pets or I misread. Both are possible, with the latter being more likely. Or perhaps I dreamed it, in which case, this is a bit embarrassing.

Thank you for the quick answers and the guide, and I'll be sure to keep a look out in the case that it happens or was someone elses pets I saw this on, now that I know it would be a bug and not strange workings.

I will note that it it is, in fact, a possible occurrence, so you weren't necessarily dreaming it up or imagining things or remembering wrong.
In species that have been revamped, it is something that you can see, since save restricted traits and the muts on most lups (the ones that had the muts before their revamp), regenerated pets can end up having completely different traits than their parents (so long as they were all extant prior to the species revamp).

examples: 1, 2, 3, 4, 5

Okay, so I did see it somewhere else. However, you're using some terms that I don't quite understand. At all, really.

What do you mean by muts? I'm thinking mutations, but that doesn't seem to be the case. What are save restricted traits? I know about generating pets, but what are regenerated pets? Also, what do you mean by extant? I am unfamiliar with that term.

Muts = short for mutations, yes

Restricted traits are traits that cannot (save specific ones in specific circumstances) be generated onto pets, and are obtained typically by either making Majestic theme pets during the seasonal fests, or by use of Restricted Trait Disruptors, guide to them here

Guide to regeneration here, which should contain all pertinent information on that front.

Extant = currently/still in existence (basically what we meant, "all extant prior to the species revamp" = "all existed before their species' revamp" (apparently my usage was slightly flawed semantically, but anyway))