I had it happen. I normally buy full-fare J (actually, all the time). I had a Delta trip through Atlanta (went down to Florida via AC, came back via Atlanta on Delta) and it sold me a discounted J-fare on Delta. I only learned this when I went to switch to an AC ATL-YYZ flight, and found out I couldn't use the coupon.

I think the only way to know is to look at the conditions of the ticket very carefully.