Can you perhaps post us screenshots of the 4 regionals' pokedex entries showing "caught 1 seen 1" and the candy being more than 3?
I don't know about single stage Pokemon but it is possible to hatch multistage pokemon with less than 3 candy as a freind hatched a Bulbasuar yeilding two candies.
Huh, I have a Seel that crashes my game every time I look at his stats.
This happened to me once, it was right next to the grimer that usually crashes the game. Hope the Grimer doesn't infect other pokemon or corrupted it's pokebox slot space :\