Canelli beans and chickpeas both got brown/purple spots after I cooked them...

I wonder if those were dry spots. I generally cook chickpeas in a pressure cooker, and if I've cooked them for too long or in the absence of enough water, portions of the beans dry out and it looks like the beans are spotted. The very first time that I ever made chickpeas, the top layer came out looking like Dalmatian beans and all the chickpeas beneath were uniformly darker and hard as rocks.

No canellini experience, sorry. But my guess is the same, and if it happens again, you may not need to throw it all.

Very strange especially since you said that you rinsed both beans and a visual inspection did not reveal anything odd.

That would indicate that the spots developed during the cooking which points to some sort of chemical reaction between the beans and the other ingredients (and possibly with the cooking vessel itself).

You could split some of the spotted beans open to see if there's anything inside, but it doesn't look like an insect infestation. Maybe a diseased bean plant? Possible, but very odd that it affected both the cannellini beans and the chickpeas which were canned separately. Plus, you said you didn't see anything when you rinsed the beans.

Did you change anything else with your ingredients? A different brand of something?

In any case, I would probably throw away, start again, maybe ask the merchant for a refund for the beans (show the photos).

Here’s another photo

What else was in the pot? I see tomatoes and some little seeds? Could the spots have come from prolonged contact with some kind of spice/seed in the dish that leached color onto the beans? I can't imagine that 2 different kinds of canned beans would have mold or anything that would show up on both upon further cooking, so my thought is it's something else in the dish?

OK I figured out how to add a photo. They did not look like this when I put them in I thought maybe they got Burnt but I don’t believe that is the case