It just looks like some of the prunes were too deep and cut into the branch collar. If that happens a wound can't seal up properly
Discussion
It appears on all the cuts and around dead branches. On the main trucks as well.
The only issues I typically deal with on apples around here is fireblight. Not sure what that looks like on an older tree like yours
These are the 4 main diseases with apples.. 
Thanks for the info. Yes, I've seen the scabs before for a couple of seasons..
It says in text from your book if left untreated can lead to black rot. Which maybe my case.
Can you send me the picture of what it says about black eating chapter 18?
I also lost two older pear trees to firelight 5 years ago so that could have spread. Although the apples look pretty healthy with a few scabs and aren't going scorched black like the pears did.
You got it 