Sometimes this happens to me, not just in The Wind Waker but in other Zelda games as well. What I do is get information where each thing is, then I go to each place to get it. Even if I know I'd gotten a Piece Of Heart from a ledge, I still go back and check. So what you can do for the charts is make a list like below and cross them off when you get them. Make notes if it's from a mini-game, store, hard or easy to get, etc. It's best to write it in pen and cross them off in pencil, that way you can use the list more than once.
List Of Charts In The Wind Waker:
1. Forbidden Woods - Boomerang, Deku Leaf
- Maggie's Father: give him 20 Skull Necklaces
3. Forest Haven - Deku Leaf
Rock Spire Isle
- Beedle's Shop Ship: 900 rupees
- Molgera's hideout
I hope this helps. If it doesn't, then you've most likely encountered a glitch by accident. Either let them go or start a new game. Sorry.