Whoa. You're not kidding. It actually happens on BOTH code sets. I used a clean download of 3.02 and it happens on the Wii as well.
EDIT: Okay i did some more research on this and this is how it happens.
This occurs when you select Yoshi on Classic mode.
This also occurs for all the extra and stock colors of Yoshi.
The next thing I did was to play on all of the difficulties.
So far all of them freeze before the first video of the SSE, which it doesn't do on all the other characters.
After that, i repeated all of the difficulties with at least one continue because it changes the final boss battle. And so far all of the events still froze at the SSE video.
The final thing i did was to do all of tests to BOTH of the code sets on Dolphin and the Wii. My results of this were all the same as using Dolphin.