I was trying to create a round hole in a facet by taking the difference bwetween a square and round facet. It summed the areas rather than subtracting the inner one. This throws off all the calcuated values that relies on area. Facet 1 & 2 are the original, and 3 the difference.
It worked ok if the smaller facet was square rather than round. My fix was to create the hole manually from four seperate facets, by slecting the vertices manually in the correct order. I think molflow has a problem handling shapes that are too "concave". The sum of the areas of these four new facets is correct.