How long did you let the stain sit before clear was applied? If you did 2 coats of stain you should wait 48-72 hrs before topcoat. Make sure you are carefull with sanding the clear, if you go thru to the stain it will show on the next coat, the first coat of clear is normally the most difficult as you can get airbubbles from the wood pores, subsequent coats should flow nicer, if you are not using water base poly you can also thin 10-20 % this will slow dry time and flow better giving bubbles time to off gas before the poly flashes. Pine is a pita to get consistent nice finish, took me a long time and lots of experimenting to find results I could live with, good luck and post up some pics.
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