-Try making hitboxes the same size and center
-Stop pokemon seeing through walls in the wild
-Make loot balls better like making mega stones more common
Explain to me how it's a bug, the map is draw in layers, same thing happens in all the other Pokemon games because its the easiest + fastest way to draw the game, changing the collision size will do nothing to prevent this.
also in the fire area, they sometimes see-through there too so you have to retrieve them and send them out that is annoying especially when the attack is loaded.