I keep having the problem of having books that I go to put in a collection and they stay on my home screen and will not go into the collection. It's like it just can't register the action. even with a hard reset it will not work. i've deleted and re-downloaded the books and sometimes that works. don't ask me why.
I dare say they go into the collection. . . but you probably have the sort still set to title, author, or most recent. When you sort by collections, you'll see that it will show your collections with a number that says how many books are in each and any un-collected books after that.