Looks like they were tightened down without being seated all the way. And the dowel crushed some of the casting in the head as it got tightened down.
X3 looks like somebody tightened the head bolt before they snugged the small one to make sure they were seated fully.
I like to go fast
My stock 2xx,xxx 1st Gen had these when I changed the head gasket 2 years ago. AFAIK, that head wasn't lifted from the block until that day. I think 3 of the 12 had them.