More of an 'unintended consequence', but:
If you have a faerie in a bottle, and pick up another one, and choose 'store it', you get an error that you don;t have empty bottles, but the faerie isn't released. It's just wasted. You may want to fix that for future releases, especially if a player isn't closely monitoring his bottles. All you need do, is change it so that if it can't put it in the bottle, it re-spawns it close to the player.
That, or run a check to see if there are any full bottles, before offering the choice.
In the L1 block puzzle, it's possible to misalign the block in the small room with the crystal switch. Again, I'm not sure if that's intentional, but it took me half-an-hour to realise that I botched it, with a misalign. Once I realised that, I reset the room and solved it quickly. The puzzle itself isn;t hard, just tedious; but that misalign potential has no recovery possible.