Check this thread: Beam Element connections between Two plates (2D)
And this: Simplified bolt connection with beam element and rigid constraints - #100 by FEAnalyst
Modeling bolts with beams in CalculiX is rather problematic. You may actually need 3 beams per bolt to avoid the hinge effect. And rigid body constraints may not work well with them.
Alternatively, you could use spring elements, but there can be similar issues with them.
In fact, it’s usually best to just model the bolts as simplified solids - just cylinders.