I figured Kakashi just hit Tobi at the time where he's solid ie. when he's trying to warp someone. The moment Naruto passed through him, Tobi became solid to get ready to absorb Naruto. That's when Kakashi warped the Rasengan. Though, what's really weird is the implications that Tobi might have warped Kakashi's Kamui attack when he attempted to take out the Mazou. Dimension warping a dimension warping technique? Yo dawg?

Well, I suspect we'll get an explanation from Kakashi in the next chapter about what's really going on here, then it's theory time.