I don't have a reply to your problem but something similar happened to me. I caught a Yveltal in the ghost map using a greatball. I think it was level 67, not too sure....but when i went back to "View All Your Pokemon", it wasnt there at all. The Darkrai that i caught previously can be seen but Yveltal is not there. I hate seeing one legendary pokemon missing considering I just joined the game and it's so hard to find them
I really hope the developers can do something about this issue