Amanita Design's programmer, 'Oldes', has added this suggestion to the blog
"What about resetting the iPad? Does it help? Remember, iPad has operating system how we remember it from PC era, it’s just not so visible for ordinary people. Resetting the system helps to clear memory leaks which can be in the system itself or other apps. It does not have to be problem with the Machinarium. The game is just huge and requires the memory which may be unavailable."
He has also given a link to an article titled How-To: Fix Crashing Apps on Your iPhone and iPad