I've replicated the issue with my PMDG 737 at the same airport and other third party airports and default airports.
I was able to replicate the issue and it seems to be happening after restarting coutli, since the erratic baggage and cargo loader bug I've started doing this as a work around.
This is where it gets strange though, I was able to get the issue to happen all the time but then during testing I edited the parking positions whilst I was there, since then there were no more invisible passengers even after coulti restarts and trying different airports.
It seems that after editing the parking positions i was no longer able to replicate the issue, I'll continue for now and see what happens after some flights.