My wolf Google only gave birth to two pups and I had plenty of space left in my den.

The space in your den doesn't mean you will get 3 pups. The amount of maternal of the female and charisma of the male determine how many pups you get. The higher the better the only way this would be a bug is if you used a dandelion (which makes the wolf give birth to 4 pups) and only got to.

As Golden Silence stated, the reason why you only got two pups is because of your CP. Your female currently does not have any CP in maternal, while the sire has 20 in charisma. I believe you need 30-40 CP in one of those stats to have three pups - I'm not entirely sure what the exact number is though, so don't quote me on that.

Ah, i forgot about that.