you could do this but if you break thru to the stain then your plan wont work.No waiting it out wont do anything but make you wait it might clear just a bit,but it will always be a glossy spot.
I had to redo 7 doors today took 3 hours to redo because of the drywall guys,to redo the whole thing you could sand down the side that is having the problem with 80 grit and a orbital sander,go down to the bare wood again and redo.Will turn out just fine.
you never want to try and get a thick coat the 1st time it is better to put on many thinner coats and make sure it is going ok.

hello,
moisture is trapped and is having trouble evaporating. Before you start sanding give it a few days half the time it goes away.

I would lightly sand with 220 sandpaper to break the skin of the utrethane to let the moisture out and once it clears up you can apply a thin coat of urethane to even the finish out.

If it was moisture,it would show up in more than 1 spot.Unless this an exterior door and has been in wet weather it should not have any kind of moisture content trapped inside it.
If it had any moisture your stain would of spotted up and fisheyed on you well before you even tried applying the clear.
What is happening is the cureing process is drying faster on top than underneath and it may go away,I know I said before it wont,but I gave it more thought and remebered a job we did where got some doors on too thick and the cloudyness did go away but had a more gloss effect in that spot,so we redid those doors (having a business it has to be done consitent)

when using a waterbased clear and its on to thick in some areas it apears milky. the moisture is in the product there is water in the product. if you can press your finger on the surface and it leaves a indentation that is a sign of case hardining. if that is the case it wont go away.

Thats true as being a water based,so yeah it could be too.I dont use much water base.