The lack of time is totally understandable! Just something to keep in mind if you expanded on the game later.
As for the crane bug, yes, it only happened once. It was during one of the later levels, I put the first crate down on the pad and went to get the other, but after placing the other on the pad, the minigame didn't complete. I figured it was because I didn't place the first crate on the pad well enough, so I picked up the first crate again and tried to put it in a better spot on the pad. The arm went down, but the crate didn't move with it, so it never let me place it back on the pad. Eventually I tried putting it down on a different spot away from the pad, which worked, and the minigame completed when I placed it on the floor. Hope this helps, and let me know if you need more info!