Here I have some examples that in my mind at least, don't make sense. First is Seismic Toss. It basically involves the user throwing the opponent in the air and falling on the ground. How could it not consider the Defense of the Pokemon? A Pokemon with a rock hard body will endure it much better than a Pokemon with a soft, plushy body. Blissey due to HP, can take the most Seismic Tosses. I don't think this would be possible considering her low Def. A Skarmory could easily endure it better in real life. Sky Drop on the other hand looks very much the same with Seismic Toss(both attacks lift the opponent and throw him to the ground), yet it is a physical attack and it considers Def. It doesn't make much sense.
Also, some Special moves should be Physical. Water moves in particular should be physical. Hydro Pump, Hydro Cannon, Water Pulse, Water Gun etc They are concussive thus they inflict physical damage. Hyper Voice too. It is a concussive sound blast. Draco Meteor should be physical too. Mud Bomb also. I mean guys, okay, Solar Beam is energy based. Thunder is energy based too. But the aforementioned moves obviously inflict physical damage. They aren't energy based. They are concussive and shock the body. Skarmory's body is more physically durable than that of a Blissey thus it should be able to withstand more Hydro Pumps or Mud Bombs.