You could always release the wolves/pups you don't particularly like and that don't sell. There's a little tree icon next to the pencil icon that lets you name your wolf. That little tree will let you release your wolf into the wilds of Loria. You get better rewards depending on the wolf's level too. So it could maybe help a little with funding new den slot upgrades even.
I know some people don't like releasing (like how on FR there are people who don't like exalting), but it will free up some space so you can birth some new pups. Then rinse and repeat the cycle. Though, if you don't want to release anything, I don't know how else to help except by just saving up all your pebbles and ms until you can afford a new den/slots.
Breeding is fun and I know room, especially when you're just starting out, is tight. But keep at it and you'll get more space. Hope that helps?
I'd also recommend going to the Mole Market, or flea market, and buying a bunch of the cheap companions that give you pebbles as rewards, and then pair them with your wolves and bond with them as often as possible. They also give trinkets, which you can sell to the vendor from your inventory for more pebbles as well.