The algorithm used to place items does not keep track of empty space nor try to fill them. If you require this functionality, I suggest packery.
If the size of your items are dependent on images, they can overlap if shuffle is initialized before all the images have loaded. Check out this demo to see how to fix it.
They are very similar, but I think Shuffle's filtering and sorting are easier to customize, which is the main reason I created this plugin. Isotope does have a much larger community, more tests, and more stackoverflow answers though.
Check yo' self
Try looking at the javascript files for the demos or searching the issues on GitHub.