Hi Yakov -
this is actually a very common problem in extraction - called capacitance double-counting.
Your LVS recognizes MOM capacitor as a device, so it create a device instance for MOM capacitor, described by its SPICE model (probably a very simple one).
But, your extraction tool is not instructed to exclude MOM capacitor from capacitance extraction - extraction tool treats metal lines and vias of MOM capacitor as regular interconnects, and extracts their capacitance.
This exclusion of the device from extraction is called "device blocking".
You need to check or fix your extraction setup, to enable device blocking for MOM capacitor.
Max
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