Among ninja, aside from a contest of raw strength, battle came down to intelligence and the countering of abilities.
Zetsu had long since thoroughly investigated Kakashi and Konoha's young elites.
Even Naruto's Sage Mode had been mostly documented during Jiraiya's earlier infiltration of the Rain Hidden Village.
By contrast, very little information about Konan and Obito's ninjutsu had leaked out, and neither of their abilities was conventional ninjutsu.
That gave them a natural advantage in battle. Both of them were also exceptionally good at enduring and evading, perfectly countering ninja like Kakashi and Naruto, who needed to end fights quickly.
Whoosh!
Just as Obito activated Kamui and had drawn half of Naruto's body inside, a kunai carrying a sonic boom shot in from the distant sky, aiming straight for his heart.
The fundamental principle behind the space-time ninjutsu of his right eye's Kamui was that it could absorb and release anything into and out of his unique Kamui Dimension.
His Hollowfication ability, which made him seemingly impossible to hit whenever attacked, actually worked by temporarily transferring the attacked part of his body into the Kamui Dimension, thereby avoiding damage.
However, each use of Hollowfication could not last longer than five minutes.
Whenever he used his ability to transport himself and others through space, he was actually transferring himself and those he brought into the Kamui Dimension, then using it as a transit point to reach wherever he wanted to go.
But this complete transfer into the Kamui Dimension was considerably slower than Hollowfication. Moreover, he could not use Hollowfication during the transfer and therefore could not evade attacks.
Back then, his teacher, Fourth Hokage Minato, had seen through this weakness and wounded him.
So when he saw the kunai coming, he immediately stopped casting Kamui and retreated to evade it.