This has been a problem for a long time, but now I feel like bringing it up. If you right click and delete, then the appropriate pokemon can be deleted. With Alt+click, 2 pokemon are gone. If the party's filled, slot 5 and 6 are removed by Alt+Click, then 3 and 4. I'm just now noticing this is the case after selecting a pokemon with ctrl+click. When not selecting via that, you can alt+click with no problem. Also right clicking and selecting a pokemon causes the wacky alt+click glitch.