Calculix has problems with this kind of geometry where there is contact between two cylindrical parts.
I get this a lot when I have pin to compute.
To solve this problem I usually do what Gunnar suggested me in this post (i.e., I use the compound part) Bolts shear contact not working correctly (see his first post).
I tried to write about the problem on the Calculix forum, but they suspended my account and deleted the post (I honestly don’t know why, I was neither insulting nor rude, I just rewrote what you see in the post I linked to you).
I hope this solves your problem.