Hey, thanks for taking notice of this.

I joined not that long ago and my initial instict in these games is always to look to use breeding services since usually the starter animals aren't the best but have decent kiddos.

After breeding my main wolf Atlas I would check on the mother every once in a while, and eventually saw that the kids were born, but they weren't in my den? I figured at first that maybe this is a game where they have to still stay with the mother for a time afterwards so I ignored it for a while. Just today I came back to find 2 of the three children poofed out of existance, and the remaining one was up for sale meaining it totally wasn't under my control.

I'm just looking for a little better explanation

Your female will only have 1 pup since she has 10 maternal, it takes 30 to have 3 pups, and pups can't be put up for sale on their own so either you did it and forgot or someone else was on your account

It wasn't my own female though. The pups were also up for sale by someone else, as in I had to spend even more money after the breeding cost just to save one of them.

If you breed to a female outside your pack, you don't get the pups. Unless you breed a female, the pups are born in and belong to the other pack. If you wanted the pups, you should've PMed the other pack before breeding