
Huh, that is unusual. When I revisited the Lost Kingdom, I didn't see that bird at all. If you can't find a solution on the Internet, my suggestion would be to write Nintendo a VERY DETAILED email to their customer service department about what you are experiencing. In my 30 plus years of dealing with Nintendo's customer service, they've always been very helpful. Even if they can't help you right away, your email may help them pinpoint a bug that they can then fix with a possible update patch. I think this actually happened with one of their recent 3-D Zelda games.
Worse case scenario, if you have to start the game over again, it shouldn't take you too long to get back to where you were. I was able to beat the main game in less than a week. And that's playing rather casually, too. For me, Odyssey was one of the easiest 3-D Mario titles to beat since Super Mario 3-D Land. And after beating the game, the post game rewards are well worth it, especially if you're a Mario 64 fan. I'd even say the game doesn't really even start until after you beat it.