I wanted to have a good look at what is happening at the monitored surfaces during the first race. It is possible that something is wrong with my implementation. It could be that the face orientation affects the integrals. Maybe what is positive and negative depends on that. On my car it works but that does not mean it will for every car and stl file.
Regarding your crash it looks like the coarser mesh somehow closed your exhaust. OF crashes when specified monitoring surfaces are not present. As this one seems to have disappearing during meshing MWFlow could not know in advance. You could manually modify the snappyHexMeshDict to confirm my suspicion. Somewhere it will say engine_exhaust followed by something like this (5 5), I do not know the exact number right now. Increase both numbers with one. So if it was (5 5) to (6 6). If the case now works, we spotted the problem and I can put a fix into MWFlow.