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.
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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.