The Index tutorial is not something you can avoid; it's a scripted event that occurs once you have completed four chapters. The crux of the problem is the early, incomplete research, which creates a broken state that only becomes apparent when the tutorial tries to take over.
Nintendo's official advice, while it works on a patch, is to avoid the trigger conditions entirely. This translates into one straightforward rule: do not start researching the Bewilder Bird until you have seen and completed Mr. E's Index tutorial, which happens after Chapter 4.
For completionist players eager to fill out Mr. E's book, this requires a little patience. Simply progress through the main story until the Index is fully explained to you by the game, and then feel free to investigate the Bewilder Bird and any other creatures as you please.
If you have unfortunately already encountered the bug and are stuck, the most reliable community-reported fix so far is to load a previous save file from before you made the fateful research attempt. There is no in-game button combination or trick to force-close the broken Index menu, making a prior save your only lifeline until Nintendo releases its update.
The company has apologized for the issue and has asked players for patience as it prepares a fix, but has not yet provided a timeline for when the patch will be available.
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