tbh, i really think this has to do with keldeo, genesect, and melloetta.These are the only Pokemon that are unreleased and the only way to get them is through AR. if they are removed from the pokedex mabye this will solve the error , all the other pokemon can be recieved via HG/SS/DP. so it shouldnt matter if we have those in the pokedex they are not effecting anything.