This is a great concept, and absolutely perfect for the limitation given the madness which ensued!
The tight timer led to a whole lot of fun - I initially panicked and started to move wildly, which led to me spawning a whole bunch of clones and making it practically unsolveable, but once I started to approach each stage more calmly I was able to find a solution pretty quickly.
There were a few bugs as others have pointed out, but I was still able to complete the game just fine once I'd got the hang of it. Would love to see a few more levels :)