May appear to occur due to lag; often on the next throw it will deduct two, getting back to the correct state.
The tracker flashes white at a faster rate depending on the distance to the target, but it seems that a green pulse flashes when a Pokémon spawns and is added to the tracker, though not confirmed. However, it is not related to compass or directional facing.
The HP and CP values a Pokémon is directly related to its CP increases from powering up and leveling up. Even if size and height have an effect, it is too insignificant to trump existing CP value. Size and height are also randomized upon evolution.
Rumors and Speculation
In the list of items decoded from game files, items with ItemType "ITEM_TYPE_BATTLE" and ItemCategory "ITEM_CATEGORY_BOOST" were discovered:
If enabled in the game, it is likely that these are items that will be usable in combat to increase damage, increase defense, and possibly heal your active Pokémon.
Almost every other item in the files has been confirmed in the game with the exception of 4 kinds of berry beyond Razz Berry, Master Balls, and "ITEM_TROY_DISK" that is an "ITEM_TYPE_DISK" and "ITEM_CATEGORY_DISK", so it seems likely that these are high level trainer unlocks.