There could be two things going on here:
1. Your flow simulation geometry is not lining up with your CAD geometry. You can check this with a cut plot, it will clearly demarcate the boundaries of the solid. Make sure to turn off the "use CAD geometry" option.
2. Sometimes flow trajectories just clip through valid geometry, I'm not sure why but it has to do with the way the trajectories are created. I think they are interpolated splines.