Hi,
you have two kinds of "problems" to assess:
1- the yield criterion and the associated flow rule. Before all, you of course must know which is the criterion thanks to which the program "knows" that the material has yielded. As far as I know, despite some Norms prescribe the Trescà yield criterion for some checks (e.g. the Gross Plastic Distorsion check of EN-13445), most FE programs, if not all, use the Mises yield criterion instead. If you expect the program to detect yielding with the "wrong" criterion, of course you will find a discrepancy
2- the yielding, just like all the "integrated" results (stress-related results), is calculated in the integration points of the elements (Gaussian points), NOT in the nodes. The results are generally extrapolated to the nodes using the appropriate elements formulations, but when you speak about yielding this will of course lead to irritating results, such as nodes having equivalent stress value higher than yield limit (which, with a zero-tangent-modulus "pure" plasticity, is of course nonsense!).
In order to get rid of this absurdity, you need to directly transfer the integration-points results to the nodes. Every FE program may have its own command to do that. ANSYS, for example, uses "ERESX,NO".
Please note that some programs THINK they are very clever and activate the direct transfer automatically when they detect that the element have yielded. Trouble is, that the yielding is detected element by element, not node by node, of course. So, before the algorythm detects it needs to activate the direct results transfer, it is already too late (well, I'll be a little less severe: "it MAY be already too late").
Regards