I have 2 brainstrain pods with soft spots, I'm still deliberating on whether to pluck and cut. I suspect either BER or a bug for mine. I don't have spots like yours, that said yours could just be sun tan spots, or something else not relevant to the soft spot.
I await with interest to see what others thing your problem could be :-)
By the way is it just one pod or do have more like it, and are they confined to the one plant or multiple plants?