I bred my mela female to anotjer wolf, and I used a fertility figurine on her. I got a notification that i lost the pups, so I checked how many den spaces i had. I had 3 spaces spaces

And here is the notification

mabye she had more than 3 pups and the whole litter died with her extra pups?

Maybe?

Neither of your image links are working

Unless you used a dandelion, which guarantees 4 pups, a pregnant female will naturally give birth to 1-3 pups depending on the CP placed on the maternal stat.