The software is working just like it’s supposed to. It doesn’t (moreover: can’t) know the purpose of the capacitors. The exact position of the wires on the schematic and where they connect to doesn’t matter for a netlist. The netlist is just a list of groups of things connected together and that info gets transfered to the PCB.
You have to keep the purpose of the capacitors in mind when placing the footprints on the PCB. If you go around placing them willy nilly you this is what you get.
I see that this is the same board that was reviewed in Review of my first board. @paulvdh probably asked you if you have decoupling capacitors on there just for this reason.