Waterlogue 2 renders faces much better than older versions. That said, the tips below are generally still true and can help you get the best results.
The human visual system is exquisitely tuned to recognize human faces. Slight variations (lighting, view angle, etc.) in a picture of a face are much more noticeable than similar variations in images of other things. To avoid or lessen this problem, try the following:
Use the highest resolution possible. (Pick the highest resolution available on the ruler that is to the right of the presets.)
Using the Apple Photos app, zoom in and crop your photo a bit so that the face occupies a reasonable portion of the frame before you use it in Waterlogue.
Try using a preset that has some ink outline (for example “Illustration”). This will often clarify the region around the eyes.