they just disappear from animal pen when you craft it and are left with an empty slot, basic ones craft fine however.
It sounds like a bug to me. Have you tried posting this on the bug page yet?
Actually thought I had till you mentioned 
lol
This is a known bug
Hey there Raskhaul!
This is a known issue and we’re working on a fix now. Thank you for reporting this to us. I’m really sorry for the inconvenience.
Please don’t hesitate to reach out if you encounter any other issues.
there is much better. try to make the big sand tiger
I wanted to say a word for people who didn’t know. if you add 5 identical animals. and that you feed it with shadow flowers you will have 1 boss out of the 5 for sure
hahaha xD