The triangle.mag and triangle_wrong.mag are the correct version layout and the misconnected version layout of a triangular wave generator. The triangle.spice and triangle_wrong.spice are the extracted netlists. I have drawn a rectangle around the misconnected point using comment layer. The OTA and OTA_tri are two instances used in this layout. As shown in the screenshots, the misconnected layout accidentally connects metal2 at the top level to via1 of the instance OTA, thus forming a wrong connection. But a lvs between these two spice netlist shows 'circuits match uniquely'. And in a second thought, there might be something wrong with the extraction...... here is my command for extraction:
ext2spice lvs
ext2spice