Diodes extraction problem with Calibre Interactive LVS

I work in kits which embed diode instances under the MOSFETs
so that everything that might be extracted, has its mate. I'd
expect that a lot (maybe all) of the discrepant diodes are
NWell-psub wells, which another foundry requires the designer
to manually place and set geometry properties of dnwell for
every distinct NWell region.

Are you convinced that the discrepant diodes are indeed the
N+/psub and P+/Nw, MOSFET S/D junctions and not those
"not a device" Nw/Psub (unless you look close, or bias wrong,
or are making a bandgap with substrate PNPs) features? Or,
does "no diodes" setting just happen to kill the Nw/Psub
diode errors as well?

Thank you for your answer!

As an example I attach schematic and layout of AND cell with aforementioned diodes (they are for ESD protection as I suppose). These diodes have their own recognition layer in layout view. It seems that Calibre doesn’t recognize this layer that’s why it reports about missing devices in layout (gds). But as I said it reports about absence of only part of the total number of diodes (maybe this relates with Calibre specific).
When I said that have cut off diodes I meant that I’ve commented them in netlist file so Calibre LVS can’t read them.

OK. My hot take is, those circled "diodes" are antenna diodes
baked into the standard cell layout. The recognition layer may
be to help antenna rule checks or may be to apply "special
rules" to what may be a "sub-minimum", special purpose device.

However, to my eye these diodes lack "active" and "contact"
and counter-dope layers (P+ in Nw or N+ in Pw). Maybe those
last are turned off, or Booleaned off the active*well_type, or
are line-on-line "keyholed" such that I can't make it out (I
always, always make my own private layer table with N, P
features' fill stipple and color set up so I can see them plainly -
since I'm an old bipolar analog guy and stacked juctions is
how we roll).

If those features are missing then those diodes would be
malformed and righteously unrecognized. However, I'd
hope that a well constructed extract / drc rules combo would
somehow light up "unrecognized" features for this kind of
reason.

These antenna diodes have active layer (maybe can’t be seen) but they lack of contact layer indeed. The tungsten local interconnect layer (LIL) is used instead it (you can see connection from source regions of transistors are made with this LIL layer too without contacts on MOS side, orange color). I’ve even tried to add contacts for diode but without effect. P+ and N+ layers are also turned on (pink and yellow colors on the picture respectively).

I still think that’s Calibre extraction problem because there is no errors during stream out of the gds file - all layers are read out correctly.

Thank you for your help anyway!