checking connectivity

I created an MCM design by creating and placing symbols and importing a netlist. I then used a SKILL routine to import shapes, vias and traces. In principle the design ought to be completely correct and I should not see any rats. I do see some rats but they seem to fall into two cases:

1) where the trace/via connecting to the pin does not contact the center of the pin. Apparently it is not happy that the connection does not make it to the center of the pin? However I don't see the rats for all such cases.

http://www.artwork.com/cadence/rats1.gif

2) more confusing are a number of rats that I don't know the reason for: Look at the triangular rats below. It seems to be bitching about Net8 which connects U1.16 to P1.16

http://www.artwork.com/cadence/rats3.gif

but if I click on the trace connecting the two pads I see that both pads light up.

http://www.artwork.com/cadence/rats2.gif

So why are all these rats still showing up if things are physically touching.

Is there a way to better understand what  it complains about. Since we are not manually drawing the vias and traces and shapes it is possible that our SKILL is not doing everything correctly but we are not clear as to what we are not doing correctly -- things "look' correctly.