Seems your extractor extracts the diodes separately from the electrical conducting layers (n-well & substrate), so I guess the corresponding connectivity rules are missing in your extract rules file. You must tell it -- somehow -- that in2 is identical to node 4 (its n-well), and in1 is identical to substrate.
If you can't change the extract rules file, you only can manipulate (cheat) the extracted netlist -- not a big problem for a single photo cell, but might get awesome, tedious and error-prone for a big array.