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Unfortunately, the farmer may be storing the onions for too long.

When you are looking at onions to buy, gently press the stem end to feel if the onion is cushy. If it feels soft and smells sour then you can be sure it's going to have some bad parts. Of course you can cut them off but at the price you are paying at a farmer's market it's not worth it. Maybe you could work out a deal with the farmer if you really wanted to keep buying their vegetables. It's worth a try if it's a regular thing. The farmer needs to keep selling and you want to support them.

I don't have an answer about your specific problem, but in a sort of related direction, never store onions and potatoes together. It will hasten the spoiling of both of them.

I have had the same problem. I usually buy a bag of onions and store them on my counter. I can only assume that they are a little less fresh because they are packaged in a bag.

My solution is just to cut the spoiled part out and use the rest.

"I don't have an answer about your specific problem, but in a sort of related direction, never store onions and potatoes together. It will hasten the spoiling of both of them."

I didn't know this, and I've been doing it for months. Whoops. Thanks for the tip, Terry!