I've seen this happen in multiple places– from Tetropolis to the flying beetle things in Frozen Flight– and more that I can't remember. Sometimes while standing on one of these moving platforms, Suit Link can't jump. So far I think I've only seen this happen in the deku scrub suit form. It's caused me so many deaths that I've had to start using the cheat menu to give me beat whistles at these parts.
When she appears without her lazy eye, and you call her out on her appearance, there could be more things that happens. One, her eye becomes deviated right in front of you and the doppelganger says "my eye's always been like that." Or two, she tells you she had surgery to get her lazy eye fixed, which could actually be the truth– you'd need to verify it somehow though.
People having their moles removed could also be a possibility.
Really rough that shortcuts opened don't remain when you retreat… Thought I was making progress when I opened a shortcut back to my car! Unfortunately, no :C
