it's impossible to have missing vias or shorted layers unless you made a mistake during GDS import/export.
i'm guessing that for the via problem you forgot to export the VIA layer, or exported based on heirarchy but had drawn vias on top - haha whoops that's a tricky one, but not the software's fault.
second - shorted layers? that doesn't even make sense. a layer is just a bunch of shapes all marked with a layer ID number, the software does not care if it is metal, poly, text, or passivation.. my guess is that you imported an unknown layer, and accidentally assigned the wrong layer ID to it.
no need to blame the tools - what about the old guys who cut plastic sheeting to make their layout? who do they blame when layers are shorted? the plastic sheet manufacturer?
post the gds that has missing vias, i will tell you what's wrong.