Board Thread:Theories and Speculation/@comment-35172651-20180401134411/@comment-9782468-20180511131849

Anyways, I doubt it's a plot hole.

Both of Obito's eyes had something different than Obito about them.

Kakashi had been using his eye for years, and with all his chakra funneling to it, it probably made it harder to identify with Obito's.

Obito has Hashi cells which have been implied to have let Obito keep his Mangekyo with no side-effects. So with all the Hashi chakra goin through it, it probably made it harder to identify.

Now, remember that pretty much no one in Konoha 11 have any idea who Obito is or how Kakashi got his Sharingan. Hinato would probably be able to see similarities if she actually looked for them, but she had no reason to. There was absolutely no reason for her to believe Tobi and Kakashi were similar in any way. Add to that the things masking the nature of the eyes that I mentioned above, and it's not a plot hole that the signatures weren't noticed.