Also, (I think its at this step) when I flatten my netlist is says there are warnings but does not print them. Any way to check the warnings?

Extracting opa_flat into opa_flat.ext:
opa_flat: 6 warnings
Total of 6 warnings.

Warnings are given by "feedback" entries, which are like DRC errors except use a different but similar set of commands. So "feedback why" ("feed why" for short, if you like) and "feedback find" will track down those errors and tell you what they are.

I am getting warnings of the form:

% feedback find
Feedback #1: device missing 1 terminal;
 connecting remainder to node cascode_bias_0/vss.

Is this the type of message that is generated for dummy devices with source and drain tied together? I dont have any unconnected devices and this seems to match the number of fully shorted dummy devices I have.

Yes, that's the behavior for source-drain tied devices.