Another paint question

I sprayed a number of flat wood items with a water-based paint. I am now
spraying on top coats of water-based polyurethane. With the initial top
coat, there were spots on one of the pieces, where the topcoat would not wet
the surface ... but showed a few very small beads in those spots. After
drying, I sanded the surfaces with 400 sandpaper ... making sure the areas
that did not wet were well sanded. The second topcoat wet the areas that it
had not wet the first time, but now there are a couple of areas on other
pieces that did not wet. I am using an airbrush and had to thin the
polyurethane before spraying. An ideas as to what is causing this
phenomenon?

Chuck