I assume by Nursery you mean Day Care? If so, the problem is this:
Pokémon in Day Care gain one experience point per step the player takes.
So if you were either sitting still or not moving much, it make sense because they gain experience from you walking, not how long they are in the Day Care.
As for the other question, I have no idea. I checked Bulbapedia and there is no glitch or feature that does that, so my guess would actually be some type of ultra-lag where it appears that they are there, but they aren't. There could be other reasons though.
Hope this helps you a bit. :)