This is not a crash or a visual glitch. It is a logic trap that blocks all progress, and Nintendo has acknowledged it publicly.
Nintendo's customer support account outlined a three-step sequence that causes the lockup. All three conditions must occur in order for the bug to fire:
Crucially, the bug acts like a time bomb. You can perform the early, discovery-less Bewilder Bird research and then play for hours with no sign of trouble. The game only breaks when you later hit the post-Chapter 4 tutorial checkpoint.
The workaround is straightforward but demands discipline from completionist players. Do not begin investigating the Bewilder Bird until you have completed Mr. E's Index tutorial. That tutorial is a fixed story event that happens after you finish four chapters.
In practice, focus on progressing through the main story for the first four chapters. You can freely document other creatures in the Index during those early hours. Just leave the Bewilder Bird alone until Mr. E officially teaches you how the encyclopedia works. After that, every creature in the game is safe to research.
If you have already triggered the bug and are staring at a frozen Index screen, the only reliable fix reported by players is to load an earlier save from before you made the initial Bewilder Bird investigation. Nintendo has not released a patch yet, and no in-game workaround exists to force-close the broken menu.
Nintendo has apologized to players and confirmed that an update is in development, but has not provided a release timeline. For now, prevention is the only sure protection.