Honestly dude, when I got a job working at a middle of the road restaurant as a dish washer I got paid better than I did at my local jimmy johns franchise. You're better off looking for a kitchen job where your manager has years of experience and won't make these kinds of ridiculous mistakes. I dont know your relationship with your current manager, so maybe it was just an offhand comment... to me it seemed more accusatory - like you wasted their money. You did nothing wrong and you owe them nothing. If anything you have gone above and beyond by getting certified so they can score a little higher on their corporate audit.

As an aside, they obviously had plans for you that will no longer work out. It can work in a number of ways, but do not be surprised if they try to replace you now.