When Hermione erases her parents' memories with the Memory Charm "Obliviate" she doesn't store them in a bottle for safe keeping.
To my knowledge Obliviate erases memories instead of hiding them or removing them for storage. So how could she have returned what was no longer there to return?
Edit: Did she actually use Obliviate? In the movie she clearly says "Obliviate". Is it possible to cast a spell while uttering the words to a different spell? In the first movie she tells Ron that he is saying "Wingardium Leviosa" wrong implying that the wording is the reason the spell is not working. We have seen wizards cast spells without saying the words implying that there is a level of mastery involved. However Hermione states later that she has never performed the Obliviate spell so she would have no prior experience.