There are a few idiosyncrasies of the UI that had me confused at first, for instance, the message and icon that you got once a building had gone through a whole production cycle was to collect the product manually, not to repeat the last thing you did? (I lost a cycle in my quarry because of that, as I went to upgrade it before collecting the stones... d'oh) and ......
I'm not sure exactly what happened there, but you need to refresh the browser or click "home" after a production cycle finishes before you can do anything else.
It does have a few bugs, it's best to post them on them in their forum, I think their moderator is going to hate me soon