Keep on truckin. I have found that if the plant is chock full of mature viable seeds through and through, then, it was probably pollinated by a neighboring plant etc.
If you have just a few seeds, here and there, like you described it is just the nature of the dioecious plant to attempt a self-pollination towards the end of maturity. Cannabis is genetically programmed to survive at all cost.
Right, late in flowering with very immature seeds happens. I see tiny immature seeds from, time to time, near the backside of big older colas and lower branches. One time I became livid while harvesting a plant that hide its secret identity from me--tons of big ole seedsTaNg's Thang.
You're on to something per the PH. The auto are sensitive beasts.