As was pointed out by early users, placing a cube at specific location or pointing to an existing cube with mouse was inaccurate (little off-the-mark). To address this issue, I added a cursor cube few weeks ago. It at least gives a preview of where the new cube will be placed or which existing cube will change if you press the mouse button. That alleviated the problem a bit. And moreover it highlighted the faulty behavior of the algorithm.
Yesterday I reprogrammed the mouse input algorithm to make the pointing more accurate. The algorithm of interpreting mouse input had some logic to figure out the cube nearest to camera when the mouse is pointing to cubes that are lying one behind the other along z-direction. This logic was also affecting when the cubes were not directly one behind the other. Few tweaks fixed this algorithm and now you should be able to point to the cubes more accurately.
On a different note, for past couple of months I am working on some major features and changes, which has been keeping me from deploying frequent updates to the app. The new features are proving little intricate to implement, requiring several rewrites. But I hope to publish one of them pretty soon with some limitations. So stay tuned.