Lugia is one of the most noticeable but a few others I noticed do it too. Gyarados and Moltres do it too off the top of my head. Also some of the sprites seem to be sort of tearing. If you look, it's on Cresselia's backsprite and the front and back of her shiny forms, The front of Leafy Wormadam, all of Mothim's sprites, both the front and back of normal and shiny Uxie, the backsprites of Illumise and Elgyem, and possibly more that I haven't found. Also, all of Burmy and Wormadam's shiny sprites aren't there at all. Also I've noticed that none of the gender differences are there.
Edit:I decided I'd go through the entire image file and point out what I see.
I noticed that the shiny backsprite for Steelix is a smaller image than the regular one. I didn't look at this ingame so I'm not sure what it looks like.
This also happens with every sprite for Teddiursa and Ursaring.
Also, Shiny Diglett's front and back sprites are different from the normal. And Shiny Dugtrio is tearing on both.
Normal and shiny Manaphy and Phione's back and front sprites are all tearing, too.
Tirtouga's front sprites normal and shiny tear.
All of Plusle's sprites tear, and quite disturbingly if you ask me. His ear is floating off his body.
Oh! I just tested out Lugia ingame and apparently it fixes itself. Lugia appears ontop of the enemy, which is kind of cool I guess.