By default, items in subcollections don't show up in the parent collection. In your local version of Zotero, you can toggle this behavior with the "recursiveCollections" hidden preference, but that's not possible online, i.e. the way you want this to display can't be done.

I'm pretty sure the items you are seeing at the parent level online are also in the parent collection locally.
dhercot December 4, 2014
Thanks, Indeed this was the case, I applied the technique proposed here to check which article was in the main folder: https://forums.zotero.org/discussion/37611/ref-view-in-folders-and-subfolders/.

I had also forgotten about this "recursive collections" option. Anyone passing by check it here: https://www.zotero.org/support/collections_and_tags#recursive_collections