Emerald does not have problems. Outdated
tools have problems. Basically, years ago, some hackers made the assumption that both 0xFF and 0x00 meant free space in Emerald. They were wrong. Like FireRed, 0xFF means free space. Some people have said that some areas of the 0x00 are free as well, but I don't hack Emerald, so I don't really know. Anyways, because of this assumption that 0x00 can be assumed to be free space, a number of outdated tools end up overwriting areas of the ROM that are not actually free space, and just like you would expect in literally any ROM, overwriting data that is used for sound causes sound corruption. So the way to avoid sound corruption is simple - don't allow tools to automatically overwrite space full of 0x00s.
http://www.pokecommunity.com/showthread.php?t=217054