Uppon breeding, the machine doesn't displays the real state of egg presence, instead
much like in quantum theory you need to check the state of it to be updated
this leads to situations like this to happen

-> There is an egg but you cannot see it , you check , the egg is there, you take out the egg
-> After taking out the egg the state isnt updated , you see the egg is still there.

Now because the state is only updated when you checked the egg will not be there

Fixed in an upcoming version, thanks!