Modeling Problem When I make a Bolt (stud bolt)

You’re working at too small of a scale. Scale up by 1000. Set units to meters but think millimeters. Or use the Dave Method.

I think there are some other issues you’re creating. Instead of 50 sides, use a multiple of 12. 24 for a half circle is likely more than enough.

Here’s an example done with 48 sides for the entire circle.