The biggest problem with SC3 is a save game bug that corrupts the save file. The bug is activated by deleting save data on a memory card that is older than the SC3 save data. Any saves that are made after SC3 are safe and fine to delete, but if you attempt to delete anything that was saved before SC3 the SC3 save data will become corrupt and in some cases or in certain ways unplayable. There is no known way to recover or fix this data, but there are steps that can be taken to avoid activating the bug.

The simplest solution, of course, is to just not delete data on your memory card, a strategy that has kept me in good stead for 15+ years. If you must delete save data that would trigger the bug (i.e. older save data than SC3's), you can use a second memory card to preserve your SC3 data and avoid the problem. It is safe to delete the SC3 data itself; simply load your game, put in the second memory card, and then allow the game to save data on the new/secondary memory card. Delete your original SC3 data, delete whatever other data is needed, then save the SC3 data back on your original memory card. Or simply leave it on the second memory card, and every time you want to delete data from one of them, transfer the SC3 data over to the other card in this manner.