Does anyone know what's wrong with my brothers game?

[YamiHoshi]

Ah, that's why, I didn't read it in full!
In that case, codes could be the cause, especially when reading:
"he might have used the capture other people's pokemon"
He might have used worse codes, according to the thing you've quoted.

 

[GalacticPetey]

Just a question, is is safe to trade with his HeartGold or transfer the data to Battle Revolution?

 

[YamiHoshi]

If the Cartridge doesn't crash, which is very unlikely.