In any anime recreation of a manga there are bound to be differences from Day 1. It's the conversion of format that does it, for the most part.
I still kinda wish the anime had stuck more with the manga storyline, but I suppose they couldn't keep up the production indefinitely.
(Pretty sure I've said this before, but the manga has a bit more lightheartedness to it than the anime. The anime is down right **depressing**. I like both, but good grief, there's only so much I can take.)