My guess is that they were expecting a much simpler application for a simple problem. Also for a JS game with a tiny backend, the Github project code is heavily weighted toward PHP (73% PHP vs 20% JS). Perhaps in their internal discussions, a word like "over-engineered" was brought up.
I'm not saying that it's bad code. It looks fine to me.
Other point is that the technical interview is a time to ask questions for the interviewee (when they allow). What is their development process? Do they iterate and prototype a lot, or is their process closer to waterfall? Assuming their stack is primarily PHP, do they use a framework? Do they follow MVC? Do they use a JS framework? Etc... Having known the answers to these questions would have helped you create an application that looked closer to their comfort zone. (Even if you don't know a coding test is coming, you still should want to know the answers to these questions so that you can know if you are getting into a situation where you might have to maintain old applications written in PHP 4, for instance.)