Ingredients "regenerating" ?

I use the "An abandoned Shack" as a house to store stuffs. On the table of the Shack, there're 2 pearls and 1 coda flower. After collecting them, when i come back after a while they're back. I suppose it's because they are ingredients as i "tidied" the place of bottles and goblets on the table and they are not coming back.

Not really important but well...