I'm experiencing a variety of bugs myself as well.
1. When putting my save file into PKHeX I've noticed that some of my Pokemon I've already caught in game contain a Legality Error. The error is always a mismatch with with origin location.
2. Some Pokemon when created will disappear after export. I created a shiny Toxtricity and it was gone by the time I imported and ran the game again. (I was able to do it the second time though.)
3. When selecting check all for the Pokedex it appears it didn't actually do it in game as well.
4. Sometimes the shiny value doesn't apply in game.
That's all I've noticed so far, I'll update my post as I notice things.
