One is that you can apply preload (pre-tension section) but the beam itself will be deleted then:
For beam elements a linear multiple point constraint is created between the nodes belonging to the beam element. The beam element itself is deleted,i.e. it will not show up in the frd-file. Therefore, no other boundary conditions or loads can be applied to such elements. Their only reason of existence is to create an easy means in which the user can define a pretension.
There are also some bugs related to beam elements in CalculiX. A few have been fixed but you can still find the rest here: GitHub ยท Where software is built
They may not go well with couplings connecting them to the model either.
And if you search this forum, you will see several attempts to model bolted and riveted connections in different ways with more or less success. Maybe try it on your case (you can define beams and 2-node springs with keyword edits).
Some threads that you may want to check:
https://prepomax.discourse.group/t/quick-connection-of-assembled-parts/2058
https://prepomax.discourse.group/t/modeling-bolt-connection-with-preloaded-beam-element/1412
https://prepomax.discourse.group/t/best-way-to-find-force-in-bolted-connection/1498
https://prepomax.discourse.group/t/beam-element-connections-between-two-plates-2d/2821
https://prepomax.discourse.group/t/creating-joints-on-assembly-meshes/2139