If the sides were not bent exactly the same, that could account for the offset. Possibly after the sides were bent, one relaxed more than the other. Trace the shape of one side on a piece of paper, and see how the other side matches up to the tracing. I wouldn't worry about it too much, now that it's done. If you were planning to keep it, play it and don't worry about it. I know where the flaws are in both of mine, and someone who built one would spot them quick enough, but I've been playing them all these years and not given it much thought.
If this was ordered by a customer, you have a dilemma. You can offer the customer a right to refuse it, and build them another one. Or offer it to them at a discounted price, if they prefer. What happens to the doughnuts that break open when they are filled with jelly? I never see them in the bakery. Appliance stores have a scratch and dent sale, you could call it a blemished instrument, and ask if they can spot the defect. Offer it at a discount, and someone will buy it.
Don't beat yourself up, it's a learning experience. And an excuse to build another one. I've been looking for an excuse to build another one myself, maybe I should show the flaws in mine to the Comptroller-Mrs.Wanda!