You need to mix the can well before using. Water based poly will have a milky color to it while it is still wet. This is due to the polyurethane resins that are used to produce the varnish. This color should go away as it dries and the molecules coalesce. putting on thick layers can cause cloudiness. Water based varnish is partly an evaporative finish, so it needs oxygen to cure. By putting on thick layers the finish will always dry from the top down. If the top dries too fast then the finish below will take much longer to dry and may cause problems down the road. Simple solution is to use more thin layers.