Board Thread:Improvements and Issues/@comment-5355747-20130313062554/@comment-26420452-20130721065907

Rukia didn't recognize him because he'd grown a beard :P

2 possible explanations:

-In the beginning, Kubo might've not decided about Isshin's and Rukia's timeline in the Gotei 13, so he concluded that she didn't know him from before, and then changed his minds about when past events occurred. (That is, a plot hole.)

- All beings with spiritual power identify people by their reiatsu, and when Rukia met him, he didn't have any at all, so she thought he was just a mere human. (No plot hole.)