The biggest most noticeable difference is in the manga Inu and Kags so not kiss. I don't honestly know what Takahashi's problem was having them do that-but she never did. It's one thing the anime has over the manga.
That and over all- kanktsu-hen was rushed. It skipped story lines, and fast forwarded through parts that had more meaning in the manga (i.e. Kagura's death. That was just glazed over in the anime), It also messed up the original time line of the story like no one's business.
Thanks for the question. ^^