Many things need to be considered to answer that question. Only you, your accountant or CRA can answer whether you are required to file or not.
But what is known is that person with zero income also can file a tax. Since your accountant already filed the tax, I would assume that he might have thought you were required to file. I see no problem in saying yes. If someone is required to file but they answered no, it could be a problem. But if someone is not required to file but still filed anyway, I don't see a problem in saying yes. It's just my opinion.