I modeled the control layout after source games such as Half-Life2 and Portal and hoped that players would be previously familiar with such. This was a failure of judgment on my part and I'm going to have it corrected in future versions.
Well, not entirely. I have played at least both Portals, so the control scheme wasn't weird. But for some reason I thought you weren't able to pick up the boxes! I think part of it is that the first puzzle is completely doable without picking the box up, just using the time rewind; in fact, if memory serves it's the easiest way to solve it. I think I tried picking it up but failed due to some bug, which made me believe you weren't able to pick it up.
Another thing that may have contributed is that the boxes look super heavy, like just a solid block of metal. There seemed to be no way that a normal person would be able to pick it up. I never played Half-Life, but in Portal the companion cubes (despite also being blocks of metal) have this sort of lightweight look to them, so it's not too surprising that you can pick them up (even if the character didn't have a specialized tool to pick them up, I feel that if I walked up to a companion cube I would be able to pick it up effortlessly). Your cube looks super dense, so I just assumed that the player would have to find ways to solve the puzzles without picking up the cube.
Maybe it was also a mistake on my part! I only saw one other comment about picking up cubes and it seems like a different problem, so it doesn't seem like a widespread issue. Don't worry about the long reply, I liked reading it, I really enjoy it when a dev takes the time to talk about the process of designing and creating the game. Good luck getting those final ratings!