I didn't read through all 25 pages, so these may have been reported already:
1. Shadow Pokemon can be hit by moves that shouldn't affect their purified typing. I was battling the Breeder in Sheridan with Shadow Duskull (since I knew he only carried Audino), and it still got hit by Secret Power and Double Slap. When I switched out to my (non-Shadow) Misdreavus, it was unaffected.
2. I was battling Valarie's Lanturn with my Mawile, and this basically is what happened:
Mawile used Sucker Punch!
But it failed!
The foe Lanturn used Thunder!
The water conducted the attack!
(animations play)
Mawile fainted!
So Sucker Punch failed even when its target selected an attack.
3. I was chasing Nim to get to Akuwa town, and (as normal), she zapped us into her dimension. However, I was completely unprepared for the battle, and I lost.
HOWEVER, after displaying the standard "game over" screen (___ scurried to a Pokemon Center...), I spawned in front of Geara, still in the psychic dimension, and I couldn't move at all and had to reset.
4. This one is small. In the Goldenleaf Gym, I ran down the right staircase from the upper level while there was a pile of books at the base, and I got stuck inside the book pile.