Without access to information on the technology you are using and the circuit you are using, I don't think a good engineering judgement is possible. but if you have lots of these errors, I would be guessing that you have a LOT of devices in your design, most of which are parasitic.. and the setting you are using are telling the simulator to treat as Shorted any resistor that is too small .. If you LOWER the number (to make the warnings go away) then you will have even more devices and the simulation will run even SLOWER..  

Now you have to put your engineering hat on and decide what is "close enough" .

jbd