i don't really understand your description of the setup or what you're expecting
could you detail out what beam joints are connected together and how they are all defined
what do the results look like if they are all rigid
have you already setup a really simple example like a cantilever to check that it isn't just this application that is affected?
I expect the beams of each joint to remain in contact about the joint. This example is a 4-post tower structure, shown above are the four base fixtures (with translation only as the BC's).
The vertical beams have Rigid end definitions, while all other have Dir 1 & 2 hinge on both ends. I'd expect allowance for the beam to rotate about the joint without a moment restraint.
When they're rigid all is fine and well.
Cantilever test does not show anything out of the norm, but it only occurs in certain areas of this model as well. Cantilever does show odd stress when ends are fixed (trans and rot) and beam is hinge - last element is 0 stress but deformation is the same as when it's rigid end condition.