Check your toolchain. I compared the Pokemon's code with one got precompiled somewhere in this post, they are the same. Also check it from my site, just in case.
This is the weird thing. I used the Yagarto thing that was linked in the github of those tools, it compiled fine. I also compiled the code.c using that, and using pokemon's exploit site it did run on my 3DS. Well, whatever, as long as the code part compiles and this thing works I am happy enough.
EDIT: Well, I quickly compared the source of pokemon's webpage to what I compiled and hosted and, well, it's the same. So either I have something screwed up in my hosting, or I dunno, maybe wrong encoding or something?