The most common way of losing donuts is accidentally speeding up a task. Did you have any long tasks going on that suddenly ended? i.e. Corn growing, Apu on a 7 day shift and Brandine birthing a Spuckler? Or maybe it was a 2 day building you sped up? It's 24 donuts to speed up a day, 48 for two, I think. It could have been partway through that.
To stop this from happening, you can turn on a notification for when you spend donuts, it asks you if you're sure you want to do it. Go to the build menu, press the little i button on the menu, turn Confirm Donut Spend on.
If, however, you have already done this, it's most likely a bug. You will have to contact EA Help to get an answer, and possibly your donuts back.