There are some unfortunate glitches related to the Tiny Chao Garden. This page will explain all of the known glitches.
Sonic Advance has a rather serious glitch which occurs when you delete the main game's save file. It prevents the rings that you earn in the main game from transferring over to the Tiny Chao Garden. This can make it a lot more difficult to earn rings for spending, as you can then only get them from playing minigames! Please be very careful when deleting your save file.
This is how the glitch works. The number of rings that you have is stored within both your main save file, and your Tiny Chao Garden save file; for example, 50 rings and 50 rings. When you delete your main save file, the Tiny Chao Garden save file does not get deleted. This means that the two save files now have an out-of-sync ring count; for example, 0 rings and 50 rings. Due to a programming error, rings do not get transferred to the Tiny Chao Garden when the two save files have an out-of-sync ring count.
You can fix the glitch if you manage to collect the right number of rings in the main game so that it matches the Tiny Chao Garden's ring count exactly — not a single ring more or less.
Sonic Adventure 2 Battle
Sonic Adventure 2 Battle also contains a serious bug. As explained on the Linking page, you can transfer Chao and items back and forth between the GameCube and Game Boy Advance games. However, Sonic Adventure 2 Battle fails to save the game after a "Pick up", and instead only saves after a "Drop off", "Move", or "Good-bye"! The Tiny Chao Garden correctly saves in all cases. This can have serious consequences if you aren't aware of it.
If you transfer anything from your Tiny Chao Garden over to Sonic Adventure 2 Battle, and then turn off your GameCube (or your game freezes), you will have permanently lost everything that you transferred! This is because the Tiny Chao Garden will have correctly saved that it no longer has the Chao or items, but the regular Chao Garden will not have saved that it received the Chao or items. If this happens to you, there is no way to get back what you lost.
To avoid this issue, you should manually save the game right away by exiting the regular Chao Garden in Sonic Adventure 2 Battle immediately after transferring anything over. You only need to do this after a "Pick up", not after a "Drop off". Alternatively, you can transfer your Chao to Sonic Adventure DX instead, as the glitch has been fixed in that game.