I'm sorry it took me so long to respond! I thawed the other bowl of frozen chili, and it tasted fine, so I'm inclined to agree with Oldvine that perhaps I had just gotten a sour spot in that first bowl of frozen beans.
All the same, I opted to go with Zhizara's advice and throw them out. Ok, so I didn't throw them out-- they're still in the fridge. But I decided not to eat them. I only kept them as a reference for color and texture as I work on my own chili recipe. I'm going back to the restaurant this week, and I will bring home another batch of chili, and I do plan to freeze some of it and see what happens. Maybe this time, I'll give it a good stir and freeze it quickly so as to avoid any sour spots.
Thank you again, everyone, for your answers. I really appreciate your help.