I have a few of those especially from my older more mature trees. They seem to be natural. It is usually those branches that have some physical injuries on them, caused by insects or our handling, then attacked by fungus, or simply the branch is shaded too much that the tree decided to reallocate its nutrients from those and divert them to younger vigorous growing parts, and so those branches die off naturally.
You can prune those off, make sure to sterilize your pruners with 70% isopropyl (rubbing alcohol) before and after pruning them off. Then swab with hydrogen peroxide the areas of cut (close to the trunk), and let dry and cover the cut portion with latex paint.