There are a few errors with battle sprites, due to the palettes being changed. For example, Elekid's back sprite has the light and medium shades of yellow switched around (between the 'light' and dark shades, you can see dots of the real light shade).
EDIT: Also, the Pokémon sprites going through things on the map is due to the way the graphics engine works. The game has a angled camera (which gives the perspective effect); this means that the character sprites have to always be angled towards the camera so they don't look squashed. As such, all the sprites on the map (not 3D models, like signs or houses) are actually significantly leaning backwards. Taller sprites, such as certain Pokémon, will therefore end up partially going through vertical objects.