It seems I’m stumbling across a bug in the way connections are recognized. The project above is the minimal reproducible example for it.
It happens when defining a part that has SMD pads on both sides of the PCB but which belong to different nets. In my original case, this is intended as a small edge connector. A pin header with 2 mm pin spacing fits rather well on a standard 1.6 mm thick PCB when plugging it from the edge of the PCB.
Whatever I tried, I get two warnings in the PCB view:
Netlist-Layout-Deviation: Unconnected Pads
We detected deviation(s) between the netlist and the processed layout of your pcb. At least one pad of each listed net is not conductively connected to it. Please check your layout before ordering. We modify the test data accordingly. See also our help article.
/net2
Netlist-Layout-Deviation: Shorted Pads
We detected deviation(s) between the netlist and the processed layout of your pcb. At least one of the listed nets shares at least one pad, which is conductively connected the other net. Please check your layout before ordering. See also our help article.
/net1, /net2_1
I checked everything but I am pretty sure both warnings are incorrect. The warnings are the same, regardless whether I upload the .kicad_pcb file, or an ODB++ export.