Shifu mentions that the dragon scroll prophecy has been around for 500 years, yet Po mention's in the first film that they've been waiting 1000 years for the Dragon scroll to be revealed. And seeing how Po is the biggest Kung fu fan, he shouldn't have been wrong.
Mr. Ping mentioned that he raised Po for 20 years before he told Po he was adopted. However, according to director Jennifer Yuh Nelson, Po is in his 20s and according to Kung Fu Panda: Secrets of the Scroll Po was a teenager 10 years ago. However, in Kung Fu Panda 2 Shen waited 30 years to rule over Gongmen City alongside his cannon, probably since then he started to use fireworks as a weapon and it's not even mentioned or shown that Shen began to use fireworks as a weapon years before or it was less than 30 years years ago he attacked the panda village and was exiled, although Shifu mentioned Po found inner peace at such a young age.
It's shown in Kung Fu Panda 2 that Li along with the over Panda's had to hide from Shen as he was killing all of the pandas, so Li and the others made the panda village. In the film Li claims that they can't share the location of the village, as if they didn't know Shen was still alive which made sense and all. But judging how word gets around fast in this world they would've known. Then it's revealed that their village was the panda village in the flash back but how would the pandas know that seeing how Li didn't even know what Chi was until Shifu told them that flashback story. Though even the pandas have no idea what Chi is there would have been no reason for them to hide still even after Shen's death.
When Oogway fights with General Kai face to face in the Spirit World, he wrote the Chinese character Chi (Pinyin is Qi4) and pushed it to attack Kai. Since the audience (and General Kai) can see this Chinese character in the right way, that means Oogway wrote this Chinese character in the opposite way (like in a mirror), which is awkward. Is Oogway really considerate?
It could be that the shot was added flipped left to right.
The goof items below may give away important plot points.
After Po defeats Kai and the masters are freed, Po and Oogway are in the spirit world talking. Oogway says he's not leaving as he 'lives here'. Po then asks if he can go back and Oogway says he doesn't know "I've never tried". Both should know returning from the spirit world is possible because Kai has already done it.
Tigress had no prior knowledge of the location of the panda village, but somehow made it there. When Kai was attacking the temple, Tigress is seen with a scroll about the pandas, which may have helped her find it.