I wonder if it's a variation on blossom end rot (BER).

Let's try to diagnose by sacrificing at least one affected fruit.
Cut it in half vertically, through the dark section. Then post a picture of the cut surface.

I took the two bad ones off and threw them away before I saw your message. If it comes back on another tomato I'll cut one open and post a photo. Thank you for your suggestion though!

Thanks for the suggestions but it's not stink bugs. I keep a really good eye on the plants and that is one thing I can rule out.

Luckily it doesn't seem to be moving anywhere else on the plant...yet

It could be anthracnose fruit rot especially if it's the lower ones that are affected.