To assess these lids first you should do some quick checking;
- The black or brown spots do not have hairs and with a simple scratch of a utensil it appears more like a "soot".
- There is no strong off odor to the contents of the jar.
- Appears that these spots are concentrated on the lid of the jar.
- When you opened the jar there was resistance in opening the lid.
The underside of canning metal lids are protected by an enamel coating. If there are any imperfections in the enamel like tiny scratches or pinholes there can be a chemical reaction. The natural compounds in food can react with the metal in the lid to form brown or black deposits. These reactive compounds are associated with proteins in the food. When subjected to the heat of processing in a water bath or pressure canner these compounds are released. The black sulfide deposits are not harmful; they are just unattractive. Many times this reaction happens with tomatoes as the acidity is a common reactor. Unfortunately, there is nothing that will prevent these spots in future canning.
If you look at the two pictures you can see there are scratches in the lid and also notice that the spots are localized to a specific place where there is an imperfection in the enamel.
I hope that this helps those of you that have had some concerns about why this is happening to your jars.