Which version is correct, 脚趾甲 or 脚指甲?
Both 脚趾 and 脚指 mean toe.

趾 means toe and 指 means finger, and historically 脚趾 is the correct term, but because 指 is a homophone and has a very similar meaning, 脚指 is such a common mistake that in modern contexts, it could be considered correct also.

Note that this only applies to the 脚趾/脚指 pair; if you only write 指甲, it would mean "fingernail".