Is it possible for you to share the model with us?
It needs some investigation.
It is some graphical related issue.
In the attached model you have defined clearance value as 120 mm i.e. if there are multiple beam joints within a span of 120 mm then software will replace that with a single joint and the structure becomes more rigid.The stresses will have lower magnitude in this case. In other words when you calculate beam joints considering zero tolerance you will have more realistic model.
If you look at the result plots at true scale you will not see any interferences.
I modified that after the problem, if i let the span on 0 only 2 of the 4 contact nodes get bonded.