The D-Sub 9 to right contains the pinout for CAN. And As I use a flat-cable to connect to the header to Left I also did the mistake of assuming that Pin 2 on the header is pin 2 on the D-Sub 9 so my pinout is completely messed up.
Looking at the left header the actual D-Sub 9 pin sequence is 1-6-2-7-3-8-4-9-5 due to the nature of a flat cable. The error is easy to correct and have no consequence for this prototype as I need a new PCB regardless. You see the error animated below as I attached correct pin numbers for the cable to match 1:1.
It is an annoying mistake to make, but I always expect some errors on my first PCB’s of some complexity. The alternative would be to double check forever using hirendous hours and still be left with errors – in my opinion it is better to get on with it, produce PCB, correct the errors and get a new PCB.