These issues are due to the imperfections of the sound emulation; there's limited documentation that's been released from Nintendo about it. Some games sound almost perfect, like Super Smash Brothers Melee, but then again, games like Tales of Symphonia are missing channels/instruments. What are your settings in the emulator, and what are your computer specs (CPU/video/OS/ETC)?
Custom Desktop -
CPU: Intel Core i5 3570 3.4 GHz to 3.8 GHz (Turbo Boost)
GPU: MSI nVidia GTX 660 2 GB GDDR5
RAM: 8192MB DDR3 SDRAM PC2 10600 1333MHz
OS: Windows 7 Professional 64-bit
HDD: 1 TB Western Digital 7200RPM HDD
CPU: Intel Core i5 3570 3.4 GHz to 3.8 GHz (Turbo Boost)
GPU: MSI nVidia GTX 660 2 GB GDDR5
RAM: 8192MB DDR3 SDRAM PC2 10600 1333MHz
OS: Windows 7 Professional 64-bit
HDD: 1 TB Western Digital 7200RPM HDD