To avoid extracting parasitics (R, C) that are accounted for in compact (SPICE) models, parasitic extraction tools are doing "device blocking" - i.e. de-embedding devices, or ignoring parasitic elements associated with "intrinsic" device properties.

If device blocking is not defined properly in the extraction rule deck - bad things can happen, for example - capacitance of MIM or MOM capacitor will be counted twice (1. in parasitic extraction and 2. in compact model).

That being said - most likely Calibre extraction rule deck is not including MIM capacitor layers in its stack, and thus is not extracting plate-to-plate capacitance - please check your Calibre deck...