When upgrating my house I did so once and took just some of the items from the storage crates in which all of my stuff was thrown out. THe next day I upgraded my house again and now I have the storage crates in my house again. In them is the stuff I took out the first time plus the stuff I didn't take out yet. WHen I first took out things I started at the top of the crates so there were are few empty rows. Now, when I look into the crates I have everything put in there nicely but when I scroll down I get to the empty spaces(about 30 rows) from the first upgrade I guess and below that the stuff I didn't take out the first time.
I only realised it quiet late so I don't know if it duplicated every item I left in there, but it seems to be that way. I know for sure that items in my backpack or things I placed around the house weren't duplicated, as well as items I already took out the first time. Though there is a small group of items I'm not sure about if I took them from the crate which didn't seem to be doubled.
Stuff that was duplicated were oranges, wasabi, crops, a watering can (exactly as broken as the original one), energy drinks, furniture that I didn't put add to the house yet and that doesn't have a picture but a "place holder" caption and fertiliser