Many anime characters don't look like they've been designed by Kishi though.
I'm sure he has some involvement in the process but he obviously doesn't write story lines for fillers. Remember how Road to Ninja was specifically said to have Kishi involved? That means it was a special case and normally he doesn't have much to do with anime/movies.
There have been inconsistencies between anime and manga, as well as errors (for example, anime has shown fuinjutsu using blood, like people putting blood on scrolls to unseal weapons, which shouldn't be the case since it isn't summoning). One would think Kishi would speak up, but he is obviously too busy with the manga? Remember his latest interview? He has almost no breaks.