Most woods vary in density from place to place and the soft parts of the alder just soaked up the waterlox where the hard places didn't. If you keep applying the waterlox it will eventually develop a film finish like varnish as you have it now in spots. If that isn't what you want I would sand the surface lightly with 220 grit paper and put another coat on wiping off the excess. Waterlox is a one of the tung oil finishes and tung oil is something that needs a lot of patience to work with. It dries really slow. It might take a couple of weeks for a coat of it to dry before putting another coat on. The best way to tell if it is dry enough to recoat is to take a clean cloth and briskly rub the surface with it and see if the tung oil smell transfers to the rag. When there is no smell it is dry.