Hi Scott,
I had a look at your file and I think the issue is with the extrude cut of the hole through the stud, combined with the pattern of the body.
The three extrude features of the hole was used to cut both the ring and the stud, but then only the stud was patterned around the axis, and so the ring is not getting cut in those other two places.
To fix the issue you are having, edit the circular pattern and choose to pattern features instead of just the body of the stud.

Select the three extrude features used to create the stud and then create the pattern.

Then roll back one step before the last extrude feature of your timeline, and do a combine of the four bodies.

Then roll back to the end and edit the final extrude and set the bodies to autoselect, and the result should be:

See file attached.
Hope that helps!
Niels