This is what I understood, when tobi dematerializes, he sends his body or part of his body to another dimension......
In this chapter, Kakashi saw a crack but the crack was made (via his observation) with something sharper.. And as we know, rasengan causes circular massive damage when it lands... So kakashi knew that rasengan wasn't the cause of the crack.. Instead it was caused by the kunai that was warped by tobi in the earlier chapter.. The kunai with lightning infused chakra by kakashi.......
Moreover, Kakashi was surprised that his Kamui was stopped...Actually not stopped, more likely evaded because Kamui won't work on something that is on another dimension.. And Tobi is more likely on another dimension when he warps himself ... SO all these led to him thinking that when he stopped the Kamui or whenever tobi warps, he is on another dimension and Kakashi's kamui sends something into another dimension.... it's like Tobi's presence is in another dimension and thus when Kakashi warped rasengan, it hits tobi because the rasengan was in the same dimension as tobi (when he warps).....
This is hypothesizing that both dimension, where Kakashi warps something with his Kamui and where Tobi goes with his spacetime jutsu, is the same