It may mean it wasn't well cleaned of the fruit.

Not necessarily dead. It could be left over fruit. Also, I was stratifying some chestnut seeds one winter and noticed mold. I rinsed the seeds very briefly in a weak bleach solution, put them back in the fridge, and they were fine and sprouted in the spring.

With cold stratification, there is a balance you want to watch between too dry (desiccation) and too wet (mold). I generally put the seeds in a slightly damp paper towel. Put the paper towel in a ziplock bag that is NOT completely closed (even open, but pressed flat), and put that in the crisper. Keep an eye out for mold and make sure the paper towel doesn't go completely dry. The other option is plant it outside in the fall and cover with steel hardware cloth to keep out the critters.