Please understand that loads are incremental in ATENA. In the model, you apply the prestressing and prescribed displacements in all steps, which means you increase both the cable stress and the deformations at the same time.
Regarding the warnings, I recommend to read about the Conditional Break Criteria in section 3.8.5.1 Solution parameters of the ATENA 3D User's Manual.
With respect to the meshing, there are joints which do not belong to any line. Basically, there are 2 ways to include the loading point in the loading plate macroelement:
1. compose the top surface from 2 or 4 surfaces, such that the loading point belongs to the lines composing the surfaces. This will not allow using brick elements for the plate, but it is usually not a problem.
2. (as in some of our examples) the point does not belong to any line of the ME. Then, you have to pay attention that the generated mesh has a node at that point.
In any case, it does not make sense to divide the plate into 2 macroelements.
Regards,