One of my hatchlings is level 2 even though I've never done anything with it. This is the first time I've had such a thing happen. Any ideas or maybe something I don't know as a newbie?

I could be completely wrong on this, but from my own personal observations, I feel like the baby will have levels on it depending on the levels of the parents. Like, level 60 parents may produce babies that hatch at level 6. But again, I could be completely wrong on this, I don't know what officially influences the baby's levels.

It will gain levels depending on if you helped it hatch, if you let it hatch on its own, it will start out at level 0

I can confirm that's not the case, because I have a few level 6 hatchlings in my hatchery who I let hatch on their own.

hmm really, very odd?

I have helped all of my lunemara hatch for the health boost, but only three out of eight have been above level 0.

That's why I think it might have something to do with the parents, because the eggs I find in the wild tend to be level 0 when they hatch, but the eggs I breed from my level 60 parents tend to be level 6, and I let them all hatch on their own.

But again, that's just based on my own observations.