hi, well there was a known bug where items wouldnt get removed probably when picked up while it was mid-air (usually the first 2 seconds) which resulted in you picking up the item but not removing the item visually. (It would partially be removed though so that’s why you’d still see the item but wouldn’t get a pick up message anymore)
I fixed this for Steam but maybe not for the itch.io version..
It does sound a lot like this bug in which case you should actually have the item in your inventory. But it also sounds like that’s not the case.
Can you confirm that? Also, are you on windows or mac?