The MIM cap has no bulk connection. But its model
netlisting wants to attach the "bottom plate to X"
capacitor's other terminal to something, and you
changed the "something" to something that has now
gone away. So not surprising that you broke the
extract logic. Many PDKs have hard embedded the
assumptions about device construction, to the code.
What you want, is immaterial in this case.
Using NWell means you get to assert explicitly where
the bottom plate capacitance returns. You can short
it to psub if you choose (and choose to have the
substrate noise, with all of its infinite mystery, push
back into the circuit). But if you want to create your
own device (which is what you are doing) then you
have the responsibility to create your own extract
and lvs collateral as well. Unless you can find a
library MIM cap that's meant, and PCell creates,
over P- field.