Tomatoes in containers
I have noticed on my tomato plants, particularly on "Money Maker," black marks or stains on and in the branches. Nearby stems which have this are very hard and brittle and snap rather than break when removed. In addition, I found one tomato on this plant that appeared rotten and removed. I have provided some photographs.
Depending on the zone you're in, tomato plants are starting to die off, so this may not be as much of an issue as you think.
One or two rotten tomatoes is to be expected in any garden, so unless you physically see pests on your plants or ALL of your fruit ends up being rotten, I wouldn't worry too much about that either.
These articles may help you identify exactly what's causing the black marks on the stems: