Net mismatch between schematic and PCB

I have just experienced an odd situation.

I did a schematic, then did the netlist (set the packages, etc.).

Read it in PCB and there were pins connections and nets that did not exist in the schematic.

So, I deleted one or two connections in the schematic and re-did the netlist and re-read it in PCB. Tried with rebuild connectivity, tried without, etc. to no avail. The bad nets were still there.

So I deleted all the connections in the schematic that appeared wrong in the PCB.

Then I added one connection, created netlist, read netlist in PCB.

Is there, some trick Iā€™m missing about making connections in the schematic?

Or did something get out sync and I just had to brute force it to recover?

For the record: KiCad 4.0.4+e1-6308~48

Regards,
Mac

On the schematic did you put No connect symbol on the unconnected pins? And ERC report no errors and warnings?

When you import your netlist in Pcbnew, did you select an option to remove single pad nets?

In at least one of the iterations I chose remove single pad nets, but it did not fix the issue.

For clarification see pins 5 & 6 highlighted below. In the PCB these two pins were connected and but net shown shown in the schematic was not.

I did not have not-connected flags anywhere, though there are non-connected pins in the schematic. These showed as warnings in the DRC. But, would that cause this sort of confusion in the netlist?

Mac

Is this a case of the deleted junction dot. Wires can appear to cross but actually be connected. In my opinion this is wrong

What does the .NET file say ?

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What happens when you select the nets as if you wer going to drag them. The highlighting shows what is actually connected

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