Heya, actually all these recipes aren't bugged. The recipes use a "trait" system, where every item in the game has traits. For example, Water is water, but it has the trait "plant food" since it can be used to make plants grow. Similarly, ice has the "water" element trait. Since there isn't an ice flower, water lily can be made with flower + ice since it would use the flower and the [water] trait from ice. The same thing happens with Wire + Spear to make thunder spear ([electricity] comes from wire).
As for the item getting stuck issue, I'm making it so the items will slowly magnetize to you when you're nearby in the next update. Sorry for the trouble with that.
And lastly, the hint system is definitely a bit lacking. I'll try to make it function better in the next update.
Sorry for the misunderstandings!