Yes, that happens. Since you go back in time, everything resets. It's not a bug or anything, and there's no way to fix it. It's the way the game works, and there's no way around it.

Think for a moment - if you were to go back in time to before doing the things that you did, then they never happened, did they? It's simple logic.

Of course, you still keep the major items you collect - the masks, your Bow, etc., just not items like Magic Beans and Deku Nuts.