My team uses an in-house portable design kit for everything, so your problem sounds very familiar.
We have schematic symbols that dump MOSFET cards with the model names "N" and "P". For LVS, we then map the model names with scripts to whatever the foundry's Calibre deck requires.
Now, in my experience, foundries tend to have LVS and PEX extract MOSFETs to subcircuit cards (whose lines start with "X"), but they are expecting the schematic to provide MOSFET cards (whose lines start with "M"), so there's some mapping going on in the Calibre deck between schematic MOSFET cards and extracted subcircuits. What we tend to see a lot is a very similar error which shows up when we forget to map the MOSFET model names to whatever the Calibre LVS or PEX deck is expecting. Looking at your netlists, you seem to have something else going on. It looks like your S-Edit netlister is netlisting your MOSFETs to subcircuit cards that start with "X", while the netlist Calibre extracted from your layout has MOSFET cards that start with "M". I expect all you have to do is change your S-Edit source schematic's MOSFET cards so they start with "M" instead of "X".