You are probably already aware of this issue, but when picking up your first item in the tutorial, it gives you the winged boots along with the blue key. Then, later, you get the real winged boots. If you pick up the second winged boots you will have 2 of them in your inventory, which takes up 3 slots. If you pick another item over the 6 slot limit, it gets completely erased from your inventory, softlocking you. It also seemingly makes the roses impossible to put in, as you all 3 roses at the same time and the clock hand to enter, softlocking you if you do the tutorial.
Edit: I figured out the source of the issue. When I exited my file where I was softlocked to the main menu, then started a new game, after I picked up the first item (the red book), the items from that softlocked file appeared in my inventory along with the book. It is taking the inventory and when picking up an item sending it to the other save file. This only happened to me in the tutorial because I have a routine of always hitting continue or load first just to see what happens.