As already mentioned above, it is very likely that stress extrapolation from the integration points inside the elements to the nodes is to blame for equivalent stresses exceeding the yield limit.
Some codes (e.g. ABAQUS) have the option to not extrapolate but just to transfer the IP values to the nearest nodes. AFAIK this is not possible in CalculiX. The effect is largest, when the boundary of the plastic zone is far from an element boundary. So you can do mesh refinement at the boundary of the plastic zone.
A typical feature of this effect is that the maximum equivalent stress in the model for ongoing loading may exhibit some noise. This can even lead to noisy load-displacement curves (in particular for coarse meshes).
If you want to examine the integration point values from the dat file, note that you also can write the coordinates of the integration points there, which allows for plots like in the sketch above.
The display of non-averaged element stresses is possible in Calculix by making sure that no node is attached to more than one element and enforce continuity by MPCs. This is what the script “separate.py” in my example collection provides.