Orochimaru's Edo Tensei on Yondaime Hokage
When Oro summoned the 1st, 2nd, and 4th Hokage with Edo Tensei, the 3rd stopped the 4th's summoning with some kind of Jutsu canceling technique. Yet it was later explained that the 4th's summoning failed because he performed Shiki Fūjin before his death, and not because of the 3rd's Jutsu canceling technique.
Kyuubi's Bijuu Dama
It is stated that the Yondaime Hokage sealed away the "Yin" part of Kyuubi's chakra with Shiki Fūjin. If that's so, then how does Kyuubi perform the Bijuu Dama with requires a mixture of "Yin" and "Yang" chakra?
The Uchiha massacre
The main reason for the massacre was because of the coup d'etat that the Uchiha were planning, but didn't the clan chose to turn their backs on Madara when he tried to fight for the Hokage's position? So why did they suddenly decided on a coup d'etat after so many years have passed?
Nagato's Rinnegan
Tobi claims that he gave his Rinnegan to Nagato, but didn't Nagato awaken his Rinnegan at a very young age when his parents were killed?
The Six Paths of Pain
Nagato pretty much turned himself into a radio tower with dozens of chakra transmitter in his body in order to control and grant 6 corpses the power of the Rinnegan. But all Tobi needed was to stick a chakra receiver into each Jinchuuriki in order to control them, not to mention that they did not manifest any of the Rinnegan's powers.
Naruto's unique Tailed-beast-mode
Why is Naruto's tailed-beast-mode so different from all 8 other Jinchuuriki although it was clearly stated that their power are the same regardless of their number of tails.
A new mysteries!
The Sharingan
Why does killing your best friend actually helps develop Mangekyou Sharingan? How did Kakashi and Sasuke develop Mangekyou Sharingan without killing their best friend (if they even have one)? How does replacing your eyes with your brother's actually makes it evolve into Eternal Mangekyou Sharingan?
Sage Mode
Why does Naruto's Sage Mode turn him into a frog while Kabuto's Sage Mode turns him into a dragon (he claims) even thou they are both sucking in the same Natural Energy?
Well, maybe killing your best friend to gain Mangekyou Sharingan was just a big-fat-lie that Itachi made up.
As for Sage Mode...maybe it's the summoning contract? But then, what will Sasuke turn into if he has Sage Mode? A man with scales and feathers? =p
1. Coincidence that he happened to cast a technique to cancel it while it was failing. Mind you the Second developed it, so the Third could have known what to do. Mind you the manga also shows no sign of the coffin at all. In a sense, it's like seeing a gun aimed at you -- just because you flinched doesn't mean they shot.
2. Naruto has chakra of his own. Perhaps the presence of the Yin influences the Kyuubi's ability to manifest abilities.
3. They turned their back on Madara for not wanting to join and make the Leaf. They were tired of fighting, pretty much. A lot changes in years, y'know? And with all the suspicion of the Uchiha, they had enough.
4. Tobi also claims to be Madara. Tobi also claimed to be a derp-kid-shinobi who liked to follow Deidara around. Case-in-point, Tobi claims a lot, and his claims aren't proven or can be yet. He could have given him the eyes in secrecy of others. Part of his plan, if anything.
5. It could be said Nagato did so to feed all of his own chakra at all times without the need of being in any danger for himself. A leader doesn't always lead his comrades into battle. Sometimes it's best to wait on the sides and see the field. Tobi also said (if memory serves) that he sees no reason to use the abilities because Naruto already faced them and knows how to counter them.
6. It doesn't say they're the same, no. It says the Kyuubi ranked them via tails. Kyuubi is (clearly) the most powerful. Likewise, Kyuubi is only his Yang chakra, so it could have an alter-effect.
7. Kakashi saw Obito die before him. Sasuke saw Itachi die before him. Perhaps it's the death of their best friend that does it. The sight of such strife, after all. As far as replacing your eyes with your sibling for the EMS? That's a bit too much to ask from us. Maybe it's the fact that it's more compatible with one-another since they're so close in blood, etc.
8. Different affinities? Different styles of using it? Why can some people do certain jutsu others can't if they're still just using chakra? A kunai is a kunai in every village; how you use it depends on you and your sensei.